Variant report

Variant	rs2945965
Chromosome Location	chr19:37027504-37027505
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:37020966..37023894-chr19:37025965..37028005,2	K562	blood:
2	chr19:37026011..37027946-chr19:37031327..37033771,2	K562	blood:
3	chr19:37019843..37021429-chr19:37026140..37028875,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs2052730	0.81[AMR][1000 genomes]
rs2385796	0.85[CHB][hapmap]
rs2912422	0.85[CHB][hapmap]
rs2912424	0.82[AMR][1000 genomes]
rs2912428	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs2912434	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2912436	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2912437	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2912445	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2945946	0.83[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2945960	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2945967	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2945968	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2945970	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs2945974	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2945977	0.96[YRI][hapmap];0.88[EUR][1000 genomes]
rs2945979	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs2945988	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs2967435	0.96[CEU][hapmap];0.90[CHB][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2967441	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2967449	0.89[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2967450	0.90[CEU][hapmap];0.92[JPT][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2967451	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs2967452	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2967462	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2967471	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2967505	0.83[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2967544	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs3107237	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs3108196	0.81[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833816	chr19:36824257-37034287	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	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
3	nsv911648	chr19:36914171-37047472	Weak transcription Active TSS Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	nsv1056134	chr19:37022039-37056943	Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2945965	ARHGEF1	cis	cerebellum	SCAN
rs2945965	PRR19	cis	cerebellum	SCAN
rs2945965	PPP1R14A	cis	cerebellum	SCAN
rs2945965	KCNK6	cis	cerebellum	SCAN
rs2945965	NFKBIB	cis	parietal	SCAN
rs2945965	MRPS12	cis	parietal	SCAN
rs2945965	IL29	cis	parietal	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37020400-37034600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:37020600-37027600	Weak transcription	Hela-S3	cervix
3	chr19:37021400-37061600	ZNF genes & repeats	Liver	Liver
4	chr19:37021600-37030000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
5	chr19:37022800-37061200	ZNF genes & repeats	Adipose Nuclei	Adipose
6	chr19:37023000-37061800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
7	chr19:37023200-37031800	ZNF genes & repeats	A549	lung
8	chr19:37023200-37032600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:37023200-37048400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr19:37023200-37060200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
11	chr19:37023200-37061600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr19:37023400-37030000	Strong transcription	Placenta Amnion	Placenta Amnion
13	chr19:37023400-37030200	ZNF genes & repeats	Fetal Intestine Small	intestine
14	chr19:37023400-37048800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr19:37023400-37060000	ZNF genes & repeats	Fetal Lung	lung
16	chr19:37023400-37062000	ZNF genes & repeats	Fetal Brain Female	brain
17	chr19:37023400-37063000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
18	chr19:37023600-37061000	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
19	chr19:37023800-37033000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr19:37023800-37057800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr19:37023800-37058200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr19:37023800-37058200	ZNF genes & repeats	Dnd41	blood
23	chr19:37023800-37061600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr19:37024000-37030600	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
25	chr19:37025400-37030200	ZNF genes & repeats	Fetal Muscle Trunk	muscle
26	chr19:37025400-37052400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
27	chr19:37025600-37027600	Strong transcription	NHDF-Ad	bronchial
28	chr19:37025600-37027800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr19:37025600-37028000	ZNF genes & repeats	Brain Substantia Nigra	brain
30	chr19:37025600-37029600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
31	chr19:37025600-37030600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
32	chr19:37025600-37032800	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
33	chr19:37025600-37049000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
34	chr19:37025600-37053000	ZNF genes & repeats	Brain Anterior Caudate	brain
35	chr19:37025600-37061000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
36	chr19:37025600-37062800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr19:37025800-37027800	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
38	chr19:37025800-37027800	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr19:37025800-37027800	ZNF genes & repeats	Aorta	Aorta
40	chr19:37025800-37027800	ZNF genes & repeats	Pancreas	Pancrea
41	chr19:37025800-37027800	ZNF genes & repeats	HSMM	muscle
42	chr19:37025800-37028000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr19:37025800-37028000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr19:37025800-37029200	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
45	chr19:37025800-37029800	ZNF genes & repeats	Fetal Muscle Leg	muscle
46	chr19:37025800-37030200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr19:37025800-37030200	ZNF genes & repeats	Brain Germinal Matrix	brain
48	chr19:37025800-37030200	ZNF genes & repeats	Ovary	ovary
49	chr19:37025800-37032600	ZNF genes & repeats	Fetal Intestine Large	intestine
50	chr19:37025800-37032800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell

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