Variant report

Variant	rs10402182
Chromosome Location	chr19:37160529-37160530
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:37155855..37159234-chr19:37160019..37162576,3	MCF-7	breast:
2	chr19:37157483..37161085-chr19:37175435..37180024,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197808	Chromatin interaction
ENSG00000189042	Chromatin interaction
ENSG00000225975	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1035777	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10403456	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10407919	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11084861	0.95[CHB][hapmap];0.84[CHD][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs11666769	0.83[ASN][1000 genomes]
rs11667894	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11668432	0.86[ASN][1000 genomes]
rs11668689	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11669816	0.90[ASN][1000 genomes]
rs11670914	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11671382	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11672098	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12608459	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12608512	0.87[ASN][1000 genomes]
rs12610555	0.85[ASN][1000 genomes]
rs12610572	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1357879	0.90[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1464830	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1464831	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1525133	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1673082	0.82[ASN][1000 genomes]
rs17272386	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1985980	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2052728	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2162296	0.95[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs2194976	0.94[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2912399	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2912408	0.83[ASN][1000 genomes]
rs2912412	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2912440	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2912442	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2912443	0.85[ASN][1000 genomes]
rs2912444	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2912446	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2945964	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2967427	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2967429	0.95[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs2967436	1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs2967437	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2967438	0.83[ASN][1000 genomes]
rs2967439	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2967440	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2967442	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2967459	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2967461	0.82[ASN][1000 genomes]
rs2967463	0.81[ASN][1000 genomes]
rs2967464	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2967473	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs3096620	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3096637	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3108593	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3108605	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35299345	0.86[ASN][1000 genomes]
rs4806338	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4806339	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4806348	0.86[EUR][1000 genomes]
rs4806349	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55940011	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55965207	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60213885	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60297398	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61457535	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61628442	0.83[ASN][1000 genomes]
rs6510551	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66717711	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66783290	0.90[ASN][1000 genomes]
rs67258954	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67995015	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs68012004	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7246216	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7251805	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73609113	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7507224	0.95[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs8100381	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8108985	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs826987	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv529817	chr19:36930549-37654062	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv833817	chr19:36978852-37195695	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
6	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
7	esv3492171	chr19:37122012-37190210	Weak transcription Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	n/a
8	esv3492172	chr19:37122562-37190060	Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	n/a
9	esv3492173	chr19:37122562-37190060	Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	n/a
10	nsv469794	chr19:37129858-37310257	Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
11	nsv482392	chr19:37129858-37310257	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers 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 target site	27 gene(s)	inside rSNPs	diseases
12	esv3420176	chr19:37130161-37207917	ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	n/a
13	nsv1061250	chr19:37134068-37188771	ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	n/a
14	esv34384	chr19:37134068-37330613	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
15	nsv817833	chr19:37146694-37357289	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10402182	ZNF285	cis	parietal	SCAN
rs10402182	ZNF567	Cis_1M	lymphoblastoid	RTeQTL
rs10402182	SARS2	cis	cerebellum	SCAN
rs10402182	HNRNPUL1	cis	parietal	SCAN
rs10402182	PSG8	cis	cerebellum	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37158400-37169000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr19:37158600-37162000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr19:37158600-37162800	Weak transcription	Brain Angular Gyrus	brain
4	chr19:37158600-37167400	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr19:37158600-37167400	Weak transcription	Psoas Muscle	Psoas
6	chr19:37158600-37168800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr19:37158600-37168800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr19:37158600-37169000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr19:37158600-37169000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr19:37158600-37169000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr19:37158600-37172800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr19:37158600-37177200	Weak transcription	Fetal Kidney	kidney
13	chr19:37158600-37177400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr19:37158600-37177400	Weak transcription	NHDF-Ad	bronchial
15	chr19:37158600-37177800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr19:37158800-37166000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
17	chr19:37159000-37162400	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr19:37159000-37177000	Weak transcription	NHLF	lung
19	chr19:37159200-37163800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr19:37159200-37163800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
21	chr19:37159200-37164600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr19:37159200-37164600	ZNF genes & repeats	Adipose Nuclei	Adipose
23	chr19:37159200-37165600	ZNF genes & repeats	Fetal Brain Female	brain
24	chr19:37159200-37166200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr19:37159200-37166200	ZNF genes & repeats	Liver	Liver
26	chr19:37159200-37168000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr19:37159200-37177600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr19:37159400-37160600	Weak transcription	Right Atrium	heart
29	chr19:37159400-37161000	Weak transcription	Fetal Intestine Large	intestine
30	chr19:37159400-37162600	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr19:37159400-37164000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr19:37159400-37177600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr19:37159600-37162200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr19:37159600-37162200	Weak transcription	Fetal Stomach	stomach
35	chr19:37159600-37162200	Weak transcription	Ovary	ovary
36	chr19:37159600-37162200	Weak transcription	Pancreas	Pancrea
37	chr19:37159600-37162400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr19:37159600-37162800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr19:37159600-37167000	Weak transcription	HSMM	muscle
40	chr19:37159600-37168800	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr19:37159600-37168800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr19:37159600-37168800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr19:37159600-37168800	Weak transcription	HSMMtube	muscle
44	chr19:37159600-37169000	Weak transcription	Placenta	Placenta
45	chr19:37159600-37176200	Weak transcription	Gastric	stomach
46	chr19:37159600-37177400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr19:37159800-37160800	ZNF genes & repeats	Brain Hippocampus Middle	brain
48	chr19:37159800-37161200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr19:37159800-37161400	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr19:37159800-37161400	Weak transcription	Thymus	Thymus

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