Variant report

Variant	rs3108192
Chromosome Location	chr19:37156604-37156605
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	chr19:37018139..37019685-chr19:37156038..37157932,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228629	Chromatin interaction
ENSG00000254004	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10402486	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11084862	0.84[EUR][1000 genomes]
rs12610353	0.81[EUR][1000 genomes]
rs1830031	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2033077	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2385642	0.84[EUR][1000 genomes]
rs2385643	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3096617	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3096618	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3096619	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3096622	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3096623	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3096627	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3096628	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3096630	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3096631	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3096632	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3096633	0.83[EUR][1000 genomes]
rs3096636	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3108166	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3108167	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3108168	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3108171	0.85[EUR][1000 genomes]
rs3108172	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3108174	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3108179	0.81[EUR][1000 genomes]
rs3108181	0.84[EUR][1000 genomes]
rs3108182	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3108184	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3108185	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3108186	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3108187	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3108188	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3108189	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3108190	0.84[EUR][1000 genomes]
rs3108191	0.84[EUR][1000 genomes]
rs3108193	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3108197	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs3108201	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs3108203	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3108205	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3108206	0.91[AFR][1000 genomes]
rs3108208	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3108209	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3108214	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs3108215	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs3108542	0.88[EUR][1000 genomes]
rs3108543	0.88[EUR][1000 genomes]
rs3108544	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3108545	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3108546	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3108550	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3108552	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3108555	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3108559	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3108560	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3108562	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3108563	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3108564	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3108565	0.81[AFR][1000 genomes]
rs3108566	0.81[EUR][1000 genomes]
rs3108567	0.81[EUR][1000 genomes]
rs3108568	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs3108570	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs3108572	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs3108574	0.81[EUR][1000 genomes]
rs3108575	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs3108576	0.81[EUR][1000 genomes]
rs3108577	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs3108579	0.81[EUR][1000 genomes]
rs3108580	0.81[EUR][1000 genomes]
rs3108594	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3108596	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3108597	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3108600	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3108602	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3108603	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3108604	0.84[EUR][1000 genomes]
rs3108607	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3108608	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3108609	0.86[EUR][1000 genomes]
rs3108610	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3111541	0.81[EUR][1000 genomes]
rs3111547	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3111549	0.83[EUR][1000 genomes]
rs3111550	0.84[EUR][1000 genomes]
rs34002069	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34395293	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4572520	0.84[EUR][1000 genomes]
rs4806336	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7245414	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7248477	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7259195	0.84[EUR][1000 genomes]
rs7259256	0.81[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3108192	ZNF567	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37134600-37157000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:37143600-37156800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr19:37145600-37156800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:37148000-37156800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr19:37149200-37156800	Weak transcription	Stomach Mucosa	stomach
6	chr19:37149600-37156800	Weak transcription	Fetal Thymus	thymus
7	chr19:37150000-37156800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr19:37150200-37156800	Weak transcription	Gastric	stomach
9	chr19:37150400-37156800	Weak transcription	Right Ventricle	heart
10	chr19:37150800-37156800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr19:37153800-37157000	ZNF genes & repeats	A549	lung
12	chr19:37154200-37157000	ZNF genes & repeats	GM12878-XiMat	blood
13	chr19:37154200-37157200	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
14	chr19:37154800-37156800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr19:37155000-37156800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr19:37155000-37156800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr19:37155000-37156800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr19:37155200-37156800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr19:37155400-37156800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr19:37155400-37156800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr19:37155400-37156800	Weak transcription	Colonic Mucosa	Colon
22	chr19:37155400-37156800	Weak transcription	Lung	lung
23	chr19:37155400-37156800	Weak transcription	Spleen	Spleen
24	chr19:37155600-37156800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr19:37155600-37156800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr19:37155600-37156800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr19:37155600-37156800	Weak transcription	Left Ventricle	heart
28	chr19:37155600-37156800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr19:37155600-37156800	Weak transcription	Small Intestine	intestine
30	chr19:37155800-37156800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr19:37155800-37156800	Weak transcription	Brain Substantia Nigra	brain
32	chr19:37155800-37156800	Weak transcription	Fetal Brain Female	brain
33	chr19:37155800-37156800	Weak transcription	Psoas Muscle	Psoas
34	chr19:37155800-37157000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr19:37156000-37156800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr19:37156000-37156800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr19:37156000-37156800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr19:37156000-37156800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr19:37156000-37156800	Weak transcription	Aorta	Aorta
40	chr19:37156000-37156800	Weak transcription	Fetal Muscle Trunk	muscle
41	chr19:37156000-37156800	Weak transcription	Fetal Muscle Leg	muscle
42	chr19:37156000-37156800	Weak transcription	Pancreas	Pancrea
43	chr19:37156000-37156800	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr19:37156000-37156800	Weak transcription	Thymus	Thymus
45	chr19:37156000-37156800	Weak transcription	HSMMtube	muscle
46	chr19:37156200-37156800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr19:37156200-37156800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr19:37156200-37156800	Weak transcription	Primary neutrophils fromperipheralblood	blood
49	chr19:37156200-37156800	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr19:37156200-37156800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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