Variant report

Variant	esv3410221
Chromosome Location	chr19:19677852-19680850
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr19:19679669-19680002	MCF10A-Er-Src	breast:	n/a	chr19:19679832-19679842 chr19:19679832-19679842 chr19:19679832-19679842 chr19:19679832-19679842
2	FOS	chr19:19679690-19679972	MCF10A-Er-Src	breast:	n/a	chr19:19679832-19679842 chr19:19679832-19679842 chr19:19679832-19679842 chr19:19679832-19679842
3	FOS	chr19:19679699-19679942	MCF10A-Er-Src	breast:	n/a	chr19:19679832-19679842 chr19:19679832-19679842 chr19:19679832-19679842 chr19:19679832-19679842
4	FOSL2	chr19:19679583-19680062	SK-N-SH	brain:	n/a	chr19:19679832-19679842 chr19:19679832-19679842 chr19:19679832-19679842 chr19:19679832-19679842
5	FOSL2	chr19:19679638-19679938	SK-N-SH	brain:	n/a	chr19:19679832-19679842 chr19:19679832-19679842 chr19:19679832-19679842 chr19:19679832-19679842
6	GATA3	chr19:19679577-19680225	SK-N-SH	brain:	n/a	n/a
7	GATA3	chr19:19679755-19680031	MCF-7	breast:	n/a	n/a
8	GATA3	chr19:19679556-19680261	SK-N-SH	brain:	n/a	n/a
9	GATA3	chr19:19679707-19680035	MCF-7	breast:	n/a	n/a
10	GATA3	chr19:19679646-19680063	T-47D	breast:	n/a	n/a
11	HA-E2F1	chr19:19679634-19680122	MCF-7	breast:	n/a	n/a
12	MAX	chr19:19679737-19680001	Hela-S3	cervix:	n/a	n/a
13	NFIC	chr19:19679645-19680033	SK-N-SH	brain:	n/a	n/a
14	PAX5	chr19:19679093-19679553	GM12878	blood:	n/a	n/a
15	POLR2A	chr19:19678680-19679644	GM12892	blood:	n/a	n/a
16	POLR2A	chr19:19678709-19679288	GM12892	blood:	n/a	n/a
17	POLR2A	chr19:19678713-19679738	GM12892	blood:	n/a	n/a
18	POLR2A	chr19:19678827-19679356	GM12878	blood:	n/a	n/a
19	POLR2A	chr19:19678512-19679715	GM12892	blood:	n/a	n/a
20	POLR2A	chr19:19678715-19679387	GM12878	blood:	n/a	n/a
21	POLR2A	chr19:19678898-19679219	GM12878	blood:	n/a	n/a
22	RAD21	chr19:19679613-19680025	Hela-S3	cervix:	n/a	n/a
23	RCOR1	chr19:19679652-19679937	Hela-S3	cervix:	n/a	n/a
24	SMC3	chr19:19679651-19679987	Hela-S3	cervix:	n/a	n/a
25	USF2	chr19:19679565-19679870	Hela-S3	cervix:	n/a	n/a
26	ZNF384	chr19:19679799-19679959	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:19677939..19679808-chr19:19773324..19775987,2	K562	blood:
2	chr19:19677983..19681463-chr19:19736578..19740981,4	MCF-7	breast:
3	chr19:19661739..19664065-chr19:19676353..19678590,2	MCF-7	breast:
4	chr19:19678113..19680461-chr19:19726754..19731026,4	MCF-7	breast:

Variant related genes	Relation type
PBX4	TF binding region
ENSG00000105726	chromatin interactions
ENSG00000064547	chromatin interactions
ENSG00000105717	chromatin interactions

Extended variants
information (count: 150 )
Associated
traits (count: 58 )

Variant overlapped rSNPs/rCNVs (count:150 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs543934458	chr19:19677867-19677868	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
2	rs1865035	chr19:19677882-19677883	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
3	rs374455055	chr19:19677886-19677887	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
4	rs180833467	chr19:19677900-19677901	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
5	rs566775025	chr19:19677916-19677917	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
6	rs546188587	chr19:19677917-19677918	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
7	rs186123146	chr19:19677927-19677928	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
8	rs559760606	chr19:19678010-19678011	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs548617873	chr19:19678056-19678057	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs528816789	chr19:19678062-19678063	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs148928174	chr19:19678163-19678164	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
12	rs191366442	chr19:19678165-19678166	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
13	rs531093242	chr19:19678169-19678170	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
14	rs550276616	chr19:19678185-19678186	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
15	rs181390205	chr19:19678186-19678187	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
16	rs532842768	chr19:19678300-19678301	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
17	rs568470138	chr19:19678322-19678323	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
18	rs537135311	chr19:19678341-19678342	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
19	rs139292987	chr19:19678352-19678353	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
20	rs185043755	chr19:19678354-19678355	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
21	rs12985142	chr19:19678371-19678372	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs181177267	chr19:19678378-19678379	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
23	rs370113683	chr19:19678382-19678383	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
24	rs535432772	chr19:19678513-19678514	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
25	rs549215325	chr19:19678566-19678567	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
26	rs577495098	chr19:19678577-19678578	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
27	rs541356344	chr19:19678606-19678607	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
28	rs148268551	chr19:19678607-19678608	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
29	rs538002332	chr19:19678627-19678628	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
30	rs186858917	chr19:19678630-19678631	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
31	rs200675946	chr19:19678666-19678667	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
32	rs75063087	chr19:19678725-19678726	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
33	rs539923186	chr19:19678772-19678773	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
34	rs539650978	chr19:19678801-19678802	Weak transcription Strong transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
35	rs553213093	chr19:19678819-19678820	Weak transcription Strong transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
36	rs553133719	chr19:19678830-19678831	Weak transcription Strong transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
37	rs573187017	chr19:19678858-19678859	Weak transcription Strong transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
38	rs190698810	chr19:19678859-19678860	Weak transcription Strong transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
39	rs34409585	chr19:19678877-19678878	Weak transcription Strong transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
40	rs201066581	chr19:19678895-19678896	Weak transcription Strong transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
41	rs34003327	chr19:19678906-19678907	Weak transcription Strong transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
42	rs562372739	chr19:19678932-19678933	Weak transcription Strong transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
43	rs575772246	chr19:19678950-19678951	Weak transcription Strong transcription Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
44	rs544432520	chr19:19679046-19679047	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
45	rs564326024	chr19:19679052-19679053	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
46	rs532905966	chr19:19679061-19679062	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
47	rs546289897	chr19:19679143-19679144	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
48	rs372058451	chr19:19679182-19679183	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
49	rs559898964	chr19:19679215-19679216	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
50	rs113461615	chr19:19679219-19679220	Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:58)

Disease	PMID	Source
Follicular lymphoma	20505157	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Non-syndromic sensorineural hearing loss	20179077	CNVD
Melanoma	18172304	CNVD
Glioblastoma multiforme	21080181	CNVD
Metanephric adenoma	20802469	CNVD
Prostate cancer	16573809	CNVD
Breast cancer	16608533	CNVD
Lung cancer	17297452	CNVD
Salivary gland adenoid cystic carcinoma	17545515	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Medulloblastoma	16783165	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Chordoma	18071362	CNVD
Ewing''s sarcoma	21437220	CNVD
Medulloblastoma	21979893	CNVD
Oligodendroglial tumors	17285580	CNVD
Oral cancer	21386901	CNVD
ovarian endometriomas	16273235	CNVD
Endometrial cancer	22040021	CNVD
Acute myeloid leukemia	16864856	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Cervical cancer	21063398	CNVD
Myelodysplastic syndrome	17634407	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Chordoma	21602918	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Cancer	21637783	CNVD
Retinoblastoma	21504564	CNVD
Ovarian cancer	21720365	CNVD
Urothelial carcinoma	21177765	CNVD
Cancer	20164919	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Basal cell lymphoma	21115979	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Medullary thyroid carcinoma	18765511	CNVD
Prostate cancer	18632612	CNVD
Autism	22495311	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	21248843	CNVD
Breast cancer	21364760	CNVD
Mycobacterial infection	18421352	CNVD
Glioblastoma multiforme	22286061	CNVD
Acute monocytic leukemia	16498392	CNVD
Lung cancer	18438408	CNVD
Barrett''s adenocarcinoma	18663352	CNVD
Liver carcinoma	19366792	CNVD
Colorectal cancer	19455253	CNVD
Lujan-Fryns syndrom	21521776	CNVD
Breast cancer	20409316	CNVD
Cancer	17160897	CNVD
Cancer	17440070	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Breast cancer	21509527	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:153 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19652000-19688400	Weak transcription	Right Atrium	heart
2	chr19:19652200-19680000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr19:19652600-19686200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr19:19659200-19686200	Weak transcription	Fetal Brain Male	brain
5	chr19:19665600-19682400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr19:19665600-19685600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr19:19666600-19679600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr19:19666800-19681000	Weak transcription	Pancreas	Pancrea
9	chr19:19667600-19679600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr19:19669200-19679600	Weak transcription	NHDF-Ad	bronchial
11	chr19:19669400-19683200	Strong transcription	Fetal Stomach	stomach
12	chr19:19669400-19683600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr19:19669600-19679600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr19:19669600-19680200	Weak transcription	Fetal Intestine Small	intestine
15	chr19:19669600-19680800	Weak transcription	Gastric	stomach
16	chr19:19671000-19686200	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr19:19671200-19678200	Weak transcription	Spleen	Spleen
18	chr19:19671200-19681000	Weak transcription	Lung	lung
19	chr19:19671200-19681800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr19:19671200-19686400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr19:19671200-19686400	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr19:19671400-19681000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr19:19671600-19679600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr19:19671600-19681600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr19:19671600-19701800	Weak transcription	Stomach Smooth Muscle	stomach
26	chr19:19672000-19704800	Weak transcription	Brain Angular Gyrus	brain
27	chr19:19672200-19682000	Strong transcription	Thymus	Thymus
28	chr19:19672400-19681600	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr19:19672600-19682400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr19:19672800-19682000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
31	chr19:19673000-19679600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr19:19673000-19680800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr19:19673400-19682600	Weak transcription	Brain Hippocampus Middle	brain
34	chr19:19673600-19679400	Weak transcription	Fetal Muscle Leg	muscle
35	chr19:19673800-19680000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr19:19674000-19678200	Weak transcription	Brain Anterior Caudate	brain
37	chr19:19674200-19689200	Weak transcription	Brain Substantia Nigra	brain
38	chr19:19674200-19690600	Weak transcription	Duodenum Mucosa	Duodenum
39	chr19:19674200-19690800	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr19:19674200-19691000	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr19:19674200-19699800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr19:19674400-19679400	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr19:19674400-19679400	Weak transcription	Fetal Thymus	thymus
44	chr19:19674400-19690600	Weak transcription	Stomach Mucosa	stomach
45	chr19:19675000-19682200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr19:19675400-19681600	Strong transcription	Primary T cells from cord blood	blood
47	chr19:19675400-19681600	Strong transcription	Brain Germinal Matrix	brain
48	chr19:19675400-19682400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr19:19675400-19682400	Strong transcription	Fetal Brain Female	brain
50	chr19:19675600-19682400	Weak transcription	Adipose Nuclei	Adipose

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