Variant report

Variant	rs3108605
Chromosome Location	chr19:37109108-37109109
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:37106532..37109386-chr19:37111281..37113629,2	MCF-7	breast:

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1035777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10402182	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]
rs10403456	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10407919	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11084861	1.00[CHB][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs11666769	0.83[ASN][1000 genomes]
rs11667894	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11668432	0.85[ASN][1000 genomes]
rs11668689	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11669816	0.90[ASN][1000 genomes]
rs11670914	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11671382	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11672098	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12608459	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12608512	0.87[ASN][1000 genomes]
rs12610555	0.85[ASN][1000 genomes]
rs12610572	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1357879	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1464830	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1464831	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1525133	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1673082	0.81[ASN][1000 genomes]
rs17272386	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1985980	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2052728	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2162296	1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs2194976	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2912399	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2912400	0.89[ASN][1000 genomes]
rs2912404	0.85[ASN][1000 genomes]
rs2912408	0.92[ASN][1000 genomes]
rs2912412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2912440	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2912442	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2912443	0.94[ASN][1000 genomes]
rs2912444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2912446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2945964	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2945978	0.81[ASN][1000 genomes]
rs2967427	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2967429	1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs2967436	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2967437	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2967438	0.92[ASN][1000 genomes]
rs2967439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2967440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2967442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2967459	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2967461	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2967463	0.90[ASN][1000 genomes]
rs2967464	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2967473	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs3096620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3096637	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3108593	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35299345	0.85[ASN][1000 genomes]
rs4806338	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4806339	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4806348	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4806349	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55940011	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55965207	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60213885	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60297398	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61457535	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61628442	0.83[ASN][1000 genomes]
rs6510551	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66717711	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66783290	0.90[ASN][1000 genomes]
rs67258954	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67995015	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs68012004	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7246216	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7251805	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73609113	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7507224	1.00[CHB][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs8100381	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8108985	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs826987	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	esv3434386	chr19:37073454-37114509	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3108605	ZNF567	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37096800-37110000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr19:37097000-37112600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr19:37097200-37109600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr19:37097200-37110000	Weak transcription	NHLF	lung
5	chr19:37098000-37118200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr19:37098000-37156000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr19:37098200-37120400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:37099000-37109200	Strong transcription	Dnd41	blood
9	chr19:37099200-37110000	Strong transcription	Brain Cingulate Gyrus	brain
10	chr19:37101400-37112800	Weak transcription	Osteobl	bone
11	chr19:37101800-37111000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr19:37102000-37118600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
13	chr19:37102200-37135200	ZNF genes & repeats	Fetal Brain Female	brain
14	chr19:37103000-37118600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
15	chr19:37103200-37109200	Weak transcription	Right Ventricle	heart
16	chr19:37103600-37112600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr19:37104400-37114200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
18	chr19:37104400-37118400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
19	chr19:37104400-37125600	ZNF genes & repeats	Brain Germinal Matrix	brain
20	chr19:37105600-37110200	Weak transcription	NHDF-Ad	bronchial
21	chr19:37105600-37115200	ZNF genes & repeats	Primary B cells from cord blood	blood
22	chr19:37106200-37109600	Strong transcription	Fetal Heart	heart
23	chr19:37106400-37115400	ZNF genes & repeats	Primary T cells from cord blood	blood
24	chr19:37106800-37110400	ZNF genes & repeats	Fetal Brain Male	brain
25	chr19:37106800-37110800	Strong transcription	HSMMtube	muscle
26	chr19:37106800-37114400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
27	chr19:37106800-37151000	ZNF genes & repeats	Adipose Nuclei	Adipose
28	chr19:37106800-37156200	ZNF genes & repeats	Liver	Liver
29	chr19:37107000-37109400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
30	chr19:37107000-37109800	Strong transcription	Fetal Muscle Trunk	muscle
31	chr19:37107000-37110200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr19:37107000-37110400	ZNF genes & repeats	Pancreas	Pancrea
33	chr19:37107000-37110600	ZNF genes & repeats	Aorta	Aorta
34	chr19:37107000-37110800	ZNF genes & repeats	Ovary	ovary
35	chr19:37107000-37111400	Strong transcription	Brain Angular Gyrus	brain
36	chr19:37107000-37111400	ZNF genes & repeats	Psoas Muscle	Psoas
37	chr19:37107000-37112000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr19:37107000-37112000	ZNF genes & repeats	Left Ventricle	heart
39	chr19:37107000-37114400	ZNF genes & repeats	Colon Smooth Muscle	Colon
40	chr19:37107000-37114600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr19:37107000-37116000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
42	chr19:37107000-37118600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
43	chr19:37107000-37120400	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
44	chr19:37107000-37120400	ZNF genes & repeats	Brain Hippocampus Middle	brain
45	chr19:37107000-37125400	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr19:37107000-37134800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr19:37107000-37152400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
48	chr19:37107200-37109400	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr19:37107200-37114400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr19:37107200-37119800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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