Variant report

Variant	rs11669006
Chromosome Location	chr19:40784859-40784860
allele	C/G
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	ELF1	chr19:40784800-40786773	GM12878	blood:	n/a	chr19:40785706-40785719
2	POLR2A	chr19:40784785-40784894	Hela-S3	cervix:	n/a	n/a
3	REST	chr19:40784619-40787303	PANC-1	pancreas:	n/a	chr19:40785994-40786004 chr19:40785201-40785214 chr19:40787050-40787063 chr19:40786402-40786415 chr19:40784931-40784941 chr19:40787050-40787063
4	POLR2A	chr19:40781762-40793937	PANC-1	pancreas:	n/a	n/a
5	POLR2A	chr19:40784859-40785051	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:40768260..40771807-chr19:40783478..40786593,4	K562	blood:
2	chr19:40783887..40786272-chr19:41107076..41108731,2	K562	blood:
3	chr19:40776468..40779839-chr19:40784717..40787633,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000205041	TF binding region
ENSG00000090006	Chromatin interaction
ENSG00000105221	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11665880	0.85[EUR][1000 genomes]
rs11666690	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666860	0.83[EUR][1000 genomes]
rs11667443	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11667768	0.85[EUR][1000 genomes]
rs11667774	0.85[EUR][1000 genomes]
rs11668006	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11668520	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11669332	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11670323	0.88[EUR][1000 genomes]
rs11670860	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11670912	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11671439	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17846842	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2356230	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28746190	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35090721	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs36058450	0.84[ASN][1000 genomes]
rs3730052	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3730055	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3730262	0.80[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs41275746	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41275748	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41275750	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs45497695	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56672337	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58094119	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59058760	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59106111	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6508937	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs66623822	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs67587726	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7245751	0.88[EUR][1000 genomes]
rs7247515	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7249819	0.85[EUR][1000 genomes]
rs7252506	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73933218	0.84[ASN][1000 genomes]
rs73933225	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73933232	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73933236	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73933237	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73933238	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73933240	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73933241	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8105478	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs873143	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs874269	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv2758499	chr19:40612420-40839520	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv2758761	chr19:40612420-40839520	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv911699	chr19:40691632-40816530	Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	esv1833489	chr19:40722123-40923908	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv1057052	chr19:40776128-40789766	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
7	esv1797453	chr19:40780963-40786797	Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	esv1005660	chr19:40784738-40790835	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40766200-40788600	Weak transcription	HSMMtube	muscle
2	chr19:40770000-40789600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:40770000-40789600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr19:40770200-40789600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr19:40770200-40790200	Weak transcription	Aorta	Aorta
6	chr19:40771400-40789400	Weak transcription	HUVEC	blood vessel
7	chr19:40771600-40786000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr19:40776000-40787400	Weak transcription	A549	lung
9	chr19:40776400-40785000	Weak transcription	NHLF	lung
10	chr19:40776600-40785800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr19:40778000-40786400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr19:40778800-40785200	Weak transcription	HMEC	breast
13	chr19:40778800-40786200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr19:40778800-40787600	Weak transcription	Hela-S3	cervix
15	chr19:40779000-40786800	Weak transcription	Dnd41	blood
16	chr19:40779400-40789600	Enhancers	Left Ventricle	heart
17	chr19:40779800-40789800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr19:40780600-40786200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr19:40781000-40785400	Weak transcription	Brain Germinal Matrix	brain
20	chr19:40781000-40785800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr19:40781000-40787800	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr19:40781200-40786000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr19:40781400-40785400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr19:40781400-40785600	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr19:40781400-40788000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr19:40781400-40788000	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr19:40781600-40785800	Enhancers	K562	blood
28	chr19:40781600-40787400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr19:40781800-40785000	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr19:40782000-40785000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
31	chr19:40782200-40789400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr19:40782400-40785000	Enhancers	Right Ventricle	heart
33	chr19:40782800-40785800	Enhancers	Liver	Liver
34	chr19:40782800-40786800	Enhancers	Primary T cells fromperipheralblood	blood
35	chr19:40783000-40785000	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr19:40783000-40785000	Enhancers	Ovary	ovary
37	chr19:40783000-40788200	Enhancers	Pancreas	Pancrea
38	chr19:40783000-40789600	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr19:40783200-40786000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr19:40783200-40787000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
41	chr19:40783200-40787400	Enhancers	Fetal Intestine Large	intestine
42	chr19:40783200-40787600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr19:40783200-40788200	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr19:40783200-40789200	Enhancers	Brain Cingulate Gyrus	brain
45	chr19:40783400-40785200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr19:40783400-40785200	Enhancers	Brain Hippocampus Middle	brain
47	chr19:40783400-40785800	Enhancers	Stomach Mucosa	stomach
48	chr19:40783400-40786600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr19:40783400-40787400	Enhancers	Lung	lung
50	chr19:40783400-40788000	Enhancers	Brain Anterior Caudate	brain

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