Variant report

Variant	rs12610332
Chromosome Location	chr19:53706984-53706985
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:53700585..53702772-chr19:53706802..53709941,3	MCF-7	breast:
2	chr19:53705415..53707075-chr19:53718366..53721132,2	MCF-7	breast:

Extended variants
information (count: 73 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10401578	0.94[CHB][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.86[TSI][hapmap]
rs10775558	0.88[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10853858	0.92[CEU][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10853859	0.88[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11084224	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11084225	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11084226	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11084227	0.94[CHB][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.86[TSI][hapmap]
rs1129002	0.87[CHB][hapmap]
rs1136205	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11666072	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11669455	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11670443	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11671568	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11671603	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11672910	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11879930	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11879932	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12462419	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12462452	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12462453	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12462484	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12982950	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12984188	0.87[CHB][hapmap]
rs12984473	0.87[CHB][hapmap]
rs17206931	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17272903	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17272966	0.87[CHB][hapmap]
rs2914371	0.91[CHB][hapmap]
rs2914372	0.81[CHB][hapmap]
rs2914376	0.87[CHB][hapmap]
rs2914378	0.87[CHB][hapmap]
rs2914383	0.82[CHB][hapmap]
rs2965242	0.81[CHB][hapmap]
rs34189836	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34535235	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35001955	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35121915	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35231505	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35653121	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4358051	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4449055	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4801964	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4801965	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4801966	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4801968	0.96[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4801969	0.83[ASN][1000 genomes]
rs4801970	0.88[CEU][hapmap];0.88[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4803064	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803065	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59782712	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62117767	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62117782	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6509733	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7245395	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7245485	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7245880	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7246839	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7247982	0.80[CHB][hapmap]
rs7260577	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7260623	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065143	chr19:53507142-53853363	Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv544063	chr19:53507142-53853363	ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv1058019	chr19:53507142-53904508	ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
4	nsv544064	chr19:53507142-53904508	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv912342	chr19:53581151-54010759	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
6	nsv1063630	chr19:53591444-54419183	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	282 gene(s)	inside rSNPs	diseases
7	nsv1055378	chr19:53603268-53951855	Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription 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	34 gene(s)	inside rSNPs	diseases
8	nsv544065	chr19:53603268-53951855	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
9	esv2762999	chr19:53665818-53709353	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1065473	chr19:53680455-53709341	Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription 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	2 gene(s)	inside rSNPs	diseases
11	esv2830362	chr19:53681132-53933147	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
12	nsv1060349	chr19:53682042-53709341	ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12610332	LILRB4	cis	parietal	SCAN
rs12610332	ZNF154	cis	cerebellum	SCAN
rs12610332	ZNF818P	cis	lung	GTEx
rs12610332	ZNF818P	cis	Artery Tibial	GTEx
rs12610332	ZNF587	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53700800-53708200	Weak transcription	Fetal Heart	heart
2	chr19:53700800-53709200	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
3	chr19:53701000-53708800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr19:53701000-53709000	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
5	chr19:53701000-53709200	ZNF genes & repeats	Fetal Intestine Small	intestine
6	chr19:53701000-53709600	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr19:53701000-53710000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
8	chr19:53701200-53709600	ZNF genes & repeats	Primary B cells from cord blood	blood
9	chr19:53701200-53713200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr19:53701400-53707000	Weak transcription	Brain Germinal Matrix	brain
11	chr19:53701400-53708200	Weak transcription	Fetal Brain Female	brain
12	chr19:53701400-53709600	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
13	chr19:53701400-53710200	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
14	chr19:53701400-53715200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
15	chr19:53701600-53709200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr19:53701600-53710200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr19:53701600-53715400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
18	chr19:53701600-53720200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
19	chr19:53701600-53724800	ZNF genes & repeats	Liver	Liver
20	chr19:53701600-53725000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
21	chr19:53701600-53725000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
22	chr19:53701800-53709000	ZNF genes & repeats	Primary T cells from cord blood	blood
23	chr19:53701800-53718400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr19:53701800-53725400	ZNF genes & repeats	Adipose Nuclei	Adipose
25	chr19:53702200-53709000	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr19:53702200-53709000	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
27	chr19:53702200-53709200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr19:53702200-53710200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
29	chr19:53702200-53715200	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
30	chr19:53702400-53709600	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
31	chr19:53702400-53724800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr19:53702600-53709200	ZNF genes & repeats	Placenta	Placenta
33	chr19:53703000-53707000	Strong transcription	Right Ventricle	heart
34	chr19:53703200-53709200	ZNF genes & repeats	Fetal Intestine Large	intestine
35	chr19:53703200-53709600	ZNF genes & repeats	Lung	lung
36	chr19:53703400-53709600	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
37	chr19:53703400-53709600	ZNF genes & repeats	Esophagus	oesophagus
38	chr19:53703400-53709600	ZNF genes & repeats	Fetal Stomach	stomach
39	chr19:53703400-53715200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
40	chr19:53703600-53709600	Strong transcription	Placenta Amnion	Placenta Amnion
41	chr19:53703600-53715000	ZNF genes & repeats	Ovary	ovary
42	chr19:53704600-53707200	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr19:53704600-53708000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr19:53705200-53715000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
45	chr19:53706000-53708600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr19:53706000-53709000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr19:53706000-53709800	ZNF genes & repeats	Fetal Lung	lung
48	chr19:53706200-53707400	Strong transcription	Dnd41	blood
49	chr19:53706200-53708800	ZNF genes & repeats	NHDF-Ad	bronchial
50	chr19:53706200-53709200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived

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