Variant report

Variant	rs11666775
Chromosome Location	chr19:20163633-20163634
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:19886225..19889076-chr19:20160261..20164492,4	MCF-7	breast:
2	chr19:20161148..20163684-chr19:20228612..20230172,2	MCF-7	breast:
3	chr19:19886850..19889020-chr19:20162387..20164184,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000267419	Chromatin interaction
ENSG00000266904	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10422898	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10854017	0.81[CHB][hapmap]
rs11666100	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11666591	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11667478	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11668674	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11668676	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11668818	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11672464	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11672489	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11672515	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11672535	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11672668	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11672921	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11673240	0.87[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11673643	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12974697	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12975652	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12975674	0.88[ASN][1000 genomes]
rs12976140	0.88[ASN][1000 genomes]
rs12976315	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12978985	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12979914	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12982378	0.83[CHB][hapmap]
rs12983286	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12983837	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12985869	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2009361	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2009363	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2017453	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2159922	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2335900	1.00[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35311460	0.86[ASN][1000 genomes]
rs62134663	0.82[ASN][1000 genomes]
rs6511077	1.00[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.85[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519535	chr19:19871250-20595412	Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
2	esv3319016	chr19:19917475-20819154	Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
3	esv3319017	chr19:19917475-20819154	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
4	nsv1061846	chr19:19946927-20595412	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
5	esv3390957	chr19:19965887-20819154	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats 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	53 gene(s)	inside rSNPs	diseases
6	nsv869122	chr19:19969851-20595412	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
7	nsv1057569	chr19:19973268-20193556	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv1059158	chr19:19973489-20576161	Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
9	nsv911319	chr19:20025940-20170214	ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv870354	chr19:20043821-20576175	ZNF genes & repeats Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
11	nsv1062018	chr19:20053658-20193556	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv1066004	chr19:20053658-20592867	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
13	nsv543932	chr19:20053658-20592867	Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
14	nsv1066564	chr19:20056348-20595412	Weak transcription Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
15	nsv1066375	chr19:20061084-20574512	Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	31 gene(s)	inside rSNPs	diseases
16	nsv543934	chr19:20061084-20574512	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	31 gene(s)	inside rSNPs	diseases
17	esv3501977	chr19:20072180-20193556	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
18	esv3501978	chr19:20072180-20193556	Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
19	nsv1057309	chr19:20072886-20595412	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
20	nsv578801	chr19:20084681-20595412	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
21	nsv1055694	chr19:20088866-20595412	Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
22	nsv578802	chr19:20091702-20595412	ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
23	nsv1066970	chr19:20093894-20164335	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
24	nsv1064400	chr19:20101052-20595412	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	33 gene(s)	inside rSNPs	diseases
25	nsv911322	chr19:20111134-20193556	Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
26	nsv1066045	chr19:20142912-20179084	Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
27	nsv911325	chr19:20151257-21071548	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	49 gene(s)	inside rSNPs	diseases
28	nsv9672	chr19:20162638-20163700	Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11666775	ZNF682	cis	Muscle Skeletal	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:20162000-20164000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr19:20162200-20163800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr19:20162200-20163800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr19:20162200-20163800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr19:20162200-20164000	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr19:20162200-20164000	Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr19:20162200-20164000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr19:20162200-20164000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr19:20162200-20164000	Active TSS	Brain Germinal Matrix	brain
10	chr19:20162200-20164000	Active TSS	NHDF-Ad	bronchial
11	chr19:20162400-20163800	Active TSS	H1 Cell Line	embryonic stem cell
12	chr19:20162400-20163800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr19:20162400-20163800	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr19:20162400-20163800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr19:20162400-20163800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr19:20162400-20163800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr19:20162400-20163800	Active TSS	Brain Substantia Nigra	brain
18	chr19:20162400-20163800	Active TSS	Colonic Mucosa	Colon
19	chr19:20162400-20163800	Active TSS	Ovary	ovary
20	chr19:20162400-20163800	Active TSS	Rectal Smooth Muscle	rectum
21	chr19:20162400-20163800	Active TSS	Right Atrium	heart
22	chr19:20162400-20163800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr19:20162400-20164000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr19:20162400-20164000	Active TSS	H9 Cell Line	embryonic stem cell
25	chr19:20162400-20164000	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr19:20162400-20164000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr19:20162400-20164000	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr19:20162600-20163800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr19:20162600-20163800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
30	chr19:20162600-20163800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr19:20162600-20163800	Active TSS	Fetal Kidney	kidney
32	chr19:20162600-20163800	Active TSS	Gastric	stomach
33	chr19:20162600-20163800	Active TSS	Psoas Muscle	Psoas
34	chr19:20162600-20163800	Active TSS	Stomach Mucosa	stomach
35	chr19:20162600-20163800	ZNF genes & repeats	GM12878-XiMat	blood
36	chr19:20162600-20163800	ZNF genes & repeats	HMEC	breast
37	chr19:20162600-20164000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr19:20162600-20164000	Active TSS	iPS-15b Cell Line	embryonic stem cell
39	chr19:20162600-20164000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr19:20162600-20164000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr19:20162600-20164200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr19:20162600-20164200	Active TSS	HUES64 Cell Line	embryonic stem cell
43	chr19:20163000-20163800	Flanking Active TSS	Primary hematopoietic stem cells	blood
44	chr19:20163200-20163800	Flanking Active TSS	Primary B cells from cord blood	blood
45	chr19:20163200-20163800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
46	chr19:20163200-20163800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
47	chr19:20163200-20163800	Flanking Active TSS	Adipose Nuclei	Adipose
48	chr19:20163200-20163800	Flanking Active TSS	Placenta Amnion	Placenta Amnion
49	chr19:20163200-20164000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
50	chr19:20163200-20164000	Flanking Active TSS	Liver	Liver

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