Variant report

Variant	rs10401822
Chromosome Location	chr19:19649007-19649008
allele	C/T
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	CTCF	chr19:19648880-19649030	GM12873	blood:	n/a	chr19:19649005-19649015
2	POLR2A	chr19:19648774-19649076	GM12878	blood:	n/a	n/a
3	POLR2A	chr19:19648736-19649286	HCT-116	colon:	n/a	n/a
4	POLR2A	chr19:19648747-19649083	A549	lung:	n/a	n/a
5	PAX5	chr19:19648878-19649101	GM12878	blood:	n/a	chr19:19648896-19648906
6	POLR2A	chr19:19648792-19649430	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr19:19648626-19649266	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr19:19648908-19649123	K562	blood:	n/a	n/a
9	POLR2A	chr19:19648798-19649115	K562	blood:	n/a	n/a
10	ZNF263	chr19:19648689-19649184	HEK293-T-REx	kidney:	n/a	n/a
11	MAX	chr19:19648861-19649427	ECC-1	luminal epithelium:	n/a	chr19:19649059-19649069
12	POLR2A	chr19:19648645-19649334	ECC-1	luminal epithelium:	n/a	n/a
13	RUNX3	chr19:19648854-19649191	GM12878	blood:	n/a	chr19:19649038-19649055
14	IRF1	chr19:19648983-19649052	K562	blood:	n/a	chr19:19649008-19649022 chr19:19649024-19649038
15	POLR2A	chr19:19648928-19649250	H1-neurons	neurons:	n/a	n/a
16	POLR2A	chr19:19648681-19649116	GM12892	blood:	n/a	n/a
17	MAZ	chr19:19648707-19649977	IMR90	lung:	n/a	chr19:19649515-19649525 chr19:19649059-19649069
18	CTCF	chr19:19648940-19649090	SK-N-SH_RA	brain:	n/a	chr19:19649005-19649015
19	CCNT2	chr19:19648946-19649057	K562	blood:	n/a	n/a
20	POLR2A	chr19:19648747-19649217	H1-hESC	embryonic stem cell:	n/a	n/a
21	ZBTB7A	chr19:19648693-19649711	ECC-1	luminal epithelium:	n/a	chr19:19649367-19649378
22	MTA3	chr19:19648680-19649174	GM12878	blood:	n/a	n/a
23	POLR2A	chr19:19648808-19649018	GM12878	blood:	n/a	n/a
24	POLR2A	chr19:19648903-19649250	GM12878	blood:	n/a	n/a
25	EGR1	chr19:19648963-19649141	GM12878	blood:	n/a	chr19:19649056-19649070 chr19:19649059-19649072 chr19:19649059-19649069 chr19:19649059-19649072
26	POLR2A	chr19:19648629-19649404	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr19:19648973-19649105	Hela-S3	cervix:	n/a	n/a
28	SP1	chr19:19648688-19649253	H1-hESC	embryonic stem cell:	n/a	chr19:19649009-19649019 chr19:19649025-19649035 chr19:19649056-19649068 chr19:19649058-19649067 chr19:19649008-19649020 chr19:19649008-19649020 chr19:19649025-19649035 chr19:19649057-19649071 chr19:19649009-19649019
29	POLR2A	chr19:19648800-19649196	HepG2	liver:	n/a	n/a
30	PBX3	chr19:19648675-19649356	SK-N-SH	brain:	n/a	n/a
31	TBP	chr19:19648946-19649243	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr19:19648756-19649285	HCT-116	colon:	n/a	n/a
33	POLR2A	chr19:19648648-19649210	SK-N-SH	brain:	n/a	n/a
34	TCF3	chr19:19648846-19649310	GM12878	blood:	n/a	n/a
35	SP4	chr19:19648869-19649195	H1-hESC	embryonic stem cell:	n/a	chr19:19649006-19649022 chr19:19649004-19649020 chr19:19649056-19649072 chr19:19649022-19649038
36	ZBTB7A	chr19:19648884-19649115	K562	blood:	n/a	n/a
37	RUNX3	chr19:19648899-19649267	GM12878	blood:	n/a	chr19:19649038-19649055
38	TAF1	chr19:19648925-19649270	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr19:19649001-19649252	SK-N-SH	brain:	n/a	n/a
40	POLR2A	chr19:19648890-19649053	A549	lung:	n/a	n/a
41	POLR2A	chr19:19648753-19649203	Hela-S3	cervix:	n/a	n/a
42	SIN3A	chr19:19648991-19649294	H1-hESC	embryonic stem cell:	n/a	chr19:19649241-19649254 chr19:19649243-19649254
43	POLR2A	chr19:19648929-19649287	H1-hESC	embryonic stem cell:	n/a	n/a
44	ZEB1	chr19:19648969-19649216	GM12878	blood:	n/a	n/a
45	CTCF	chr19:19648920-19649190	GM12872	blood:	n/a	chr19:19649005-19649015
46	POLR2A	chr19:19648680-19649483	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr19:19648655-19649125	GM12878	blood:	n/a	n/a
48	POLR2A	chr19:19648670-19649199	GM12891	blood:	n/a	n/a
49	POLR2A	chr19:19648772-19649191	H1-neurons	neurons:	n/a	n/a
50	POLR2A	chr19:19648810-19649123	K562	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:19648991-19649041	Jurkat	blood:	n/a
2	chr19:19648991-19649041	ECC-1	luminal epithelium:	n/a
3	chr19:19648991-19649041	U87	brain:	n/a
4	chr19:19648987-19649037	AG10803	skin:	n/a
5	chr19:19648987-19649037	NH-A	brain:	n/a
6	chr19:19648991-19649041	HIPEpiC	eye:	n/a
7	chr19:19648987-19649037	HUVEC	blood vessel:	n/a
8	chr19:19648991-19649041	T-47D	breast:	n/a
9	chr19:19648991-19649041	GM12891	blood:	n/a
10	chr19:19648987-19649037	NHBE	bronchial:	n/a
11	chr19:19648991-19649041	HUVEC	blood vessel:	n/a
12	chr19:19648987-19649037	AG04450	lung:	fetal
13	chr19:19648991-19649041	NB4	blood:	n/a
14	chr19:19648987-19649037	HCF	heart:	n/a
15	chr19:19648991-19649041	NHDF-neo	bronchial:	n/a
16	chr19:19648991-19649041	NT2-D1	testis:	n/a
17	chr19:19648991-19649041	Hepatocyte	liver:	n/a
18	chr19:19648987-19649037	CMK	blood:	n/a
19	chr19:19648987-19649037	SK-N-SH_RA	brain:	n/a
20	chr19:19648991-19649041	HCM	heart:	n/a
21	chr19:19648991-19649041	HL-60	blood:	n/a
22	chr19:19648991-19649041	AG04449	skin:	fetal
23	chr19:19648987-19649037	HPAEpiC	pulmonary alveolar:	n/a
24	chr19:19648987-19649037	PFSK-1	brain:	n/a
25	chr19:19648987-19649037	BE2_C	brain:	n/a
26	chr19:19648991-19649041	HCF	heart:	n/a
27	chr19:19648987-19649037	SK-N-SH	brain:	n/a
28	chr19:19648991-19649041	GM06990	blood:	n/a
29	chr19:19648991-19649041	HNPCEpiC	eye:	n/a
30	chr19:19648991-19649041	K562	blood:	n/a
31	chr19:19648987-19649037	A549	lung:	n/a
32	chr19:19648987-19649037	ECC-1	luminal epithelium:	n/a
33	chr19:19648987-19649037	T-47D	breast:	n/a
34	chr19:19648991-19649041	PrEC	prostate:	n/a
35	chr19:19648991-19649041	SK-N-SH_RA	brain:	n/a
36	chr19:19648991-19649041	ProgFib	skin:	n/a
37	chr19:19648987-19649037	HIPEpiC	eye:	n/a
38	chr19:19648987-19649037	AG09309	skin:	n/a
39	chr19:19648991-19649041	BE2_C	brain:	n/a
40	chr19:19648987-19649037	HL-60	blood:	n/a
41	chr19:19648987-19649037	AG09319	gingival:	n/a
42	chr19:19648987-19649037	Hela-S3	cervix:	n/a
43	chr19:19648991-19649041	GM12878	blood:	n/a
44	chr19:19648987-19649037	MCF10A-Er-Src	breast:	n/a
45	chr19:19648987-19649037	GM12878	blood:	n/a
46	chr19:19648987-19649037	AG04449	skin:	fetal
47	chr19:19648987-19649037	U87	brain:	n/a
48	chr19:19648991-19649041	PFSK-1	brain:	n/a
49	chr19:19648991-19649041	HPAEpiC	pulmonary alveolar:	n/a
50	chr19:19648991-19649041	HCT-116	colon:	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:19647870..19650487-chr19:19773815..19776020,2	MCF-7	breast:
2	chr19:19648360..19650075-chr19:19737805..19740650,3	MCF-7	breast:
3	chr19:19625369..19628375-chr19:19648780..19652325,4	MCF-7	breast:
4	chr19:19647280..19649688-chr19:19752870..19754432,2	MCF-7	breast:
5	chr19:19625665..19627306-chr19:19648287..19650892,2	K562	blood:
6	chr19:19641380..19649124-chr19:19737025..19742358,12	MCF-7	breast:

Variant related genes	Relation type
CILP2	TF binding region
CILP2	CpG island
ENSG00000105726	Chromatin interaction
ENSG00000186010	Chromatin interaction
ENSG00000089639	Chromatin interaction
ENSG00000178093	Chromatin interaction
ENSG00000064547	Chromatin interaction
ENSG00000258674	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10403737	1.00[AMR][1000 genomes]
rs10405475	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10412351	0.84[AFR][1000 genomes]
rs10413582	1.00[AMR][1000 genomes]
rs10416335	1.00[AMR][1000 genomes]
rs10421166	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10423535	1.00[AMR][1000 genomes]
rs10425164	1.00[AMR][1000 genomes]
rs10425574	1.00[AMR][1000 genomes]
rs13344439	0.89[AMR][1000 genomes]
rs16996102	1.00[AMR][1000 genomes]
rs55927831	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59344441	1.00[AMR][1000 genomes]
rs60455087	0.89[AMR][1000 genomes]
rs73922887	1.00[AMR][1000 genomes]
rs73922890	1.00[AMR][1000 genomes]
rs73922895	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73922896	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs9304961	0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911305	chr19:19303802-19663850	Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	esv1828240	chr19:19591146-19900900	Weak transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv1063273	chr19:19591146-20061367	ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv911307	chr19:19631655-19657143	Bivalent Enhancer Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv911308	chr19:19631655-19663850	Strong transcription Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	esv1807343	chr19:19639345-19669570	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:19630600-19651800	Weak transcription	A549	lung
2	chr19:19635200-19649200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr19:19642200-19650600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr19:19643600-19675400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:19646600-19649600	Weak transcription	Brain Angular Gyrus	brain
6	chr19:19647800-19650000	Enhancers	Spleen	Spleen
7	chr19:19648000-19649800	Bivalent Enhancer	Fetal Intestine Large	intestine
8	chr19:19648000-19649800	Enhancers	Pancreas	Pancrea
9	chr19:19648200-19649200	Bivalent Enhancer	Fetal Muscle Leg	muscle
10	chr19:19648200-19649200	Bivalent Enhancer	NH-A	brain
11	chr19:19648200-19649400	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
12	chr19:19648200-19649600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr19:19648200-19649600	Enhancers	Gastric	stomach
14	chr19:19648200-19649800	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
15	chr19:19648200-19650000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
16	chr19:19648200-19650000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr19:19648200-19650000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
18	chr19:19648200-19650000	Bivalent Enhancer	Fetal Thymus	thymus
19	chr19:19648200-19650000	Enhancers	Lung	lung
20	chr19:19648200-19651400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
21	chr19:19648200-19651600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
22	chr19:19648400-19649800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
23	chr19:19648400-19649800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
24	chr19:19648400-19650000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
25	chr19:19648400-19650000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
26	chr19:19648400-19650200	Bivalent Enhancer	Placenta	Placenta
27	chr19:19648400-19651400	Bivalent Enhancer	Fetal Stomach	stomach
28	chr19:19648600-19649200	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
29	chr19:19648600-19649200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr19:19648600-19649200	Bivalent/Poised TSS	Osteobl	bone
31	chr19:19648600-19649400	Bivalent Enhancer	Brain Anterior Caudate	brain
32	chr19:19648600-19649400	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
33	chr19:19648600-19649800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr19:19648600-19649800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
35	chr19:19648600-19649800	Enhancers	Primary T killer memory cells from peripheral blood	blood
36	chr19:19648600-19649800	Bivalent Enhancer	Fetal Intestine Small	intestine
37	chr19:19648600-19649800	Bivalent Enhancer	Stomach Mucosa	stomach
38	chr19:19648600-19650000	Bivalent Enhancer	Primary T cells from cord blood	blood
39	chr19:19648600-19650000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr19:19648600-19650000	Bivalent Enhancer	Adipose Nuclei	Adipose
41	chr19:19648600-19650000	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
42	chr19:19648600-19650200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
43	chr19:19648800-19649200	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr19:19648800-19649200	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr19:19648800-19649200	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr19:19648800-19649200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
47	chr19:19648800-19649200	Bivalent Enhancer	Colon Smooth Muscle	Colon
48	chr19:19648800-19649200	Flanking Bivalent TSS/Enh	Esophagus	oesophagus
49	chr19:19648800-19649200	Active TSS	HepG2	liver
50	chr19:19648800-19649400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell

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