Variant report

Variant	rs2967505
Chromosome Location	chr19:37004938-37004939
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs17206393	0.83[GIH][hapmap];0.82[TSI][hapmap]
rs2052730	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2385796	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs2385797	0.80[MEX][hapmap]
rs2912420	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs2912422	1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs2912424	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2912426	0.86[ASN][1000 genomes]
rs2912428	1.00[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs2912431	0.88[ASN][1000 genomes]
rs2912434	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2912436	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2912437	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2912438	0.86[ASN][1000 genomes]
rs2912441	0.83[GIH][hapmap];0.82[TSI][hapmap]
rs2912445	0.91[EUR][1000 genomes]
rs2945946	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2945960	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2945965	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2945966	0.87[ASN][1000 genomes]
rs2945967	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2945968	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2945970	1.00[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs2945974	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2945977	1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2945979	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs2945980	0.81[ASN][1000 genomes]
rs2945982	0.85[ASN][1000 genomes]
rs2945987	0.85[ASN][1000 genomes]
rs2945988	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[JPT][hapmap];0.93[ASN][1000 genomes]
rs2967432	0.81[ASN][1000 genomes]
rs2967434	0.85[ASN][1000 genomes]
rs2967435	0.96[CEU][hapmap];0.85[CHB][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs2967441	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2967448	0.90[ASN][1000 genomes]
rs2967449	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2967450	0.90[CEU][hapmap];0.89[CHB][hapmap];0.92[JPT][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2967451	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2967452	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2967456	0.86[ASN][1000 genomes]
rs2967457	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2967462	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2967471	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2967474	0.86[ASN][1000 genomes]
rs2967532	0.81[JPT][hapmap]
rs2967533	0.81[JPT][hapmap]
rs2967539	0.81[GIH][hapmap];0.82[TSI][hapmap]
rs2967540	0.81[GIH][hapmap];0.82[TSI][hapmap]
rs2967542	0.81[ASN][1000 genomes]
rs2967544	1.00[CHB][hapmap];0.87[JPT][hapmap];0.86[ASN][1000 genomes]
rs3107237	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs3107238	0.87[ASN][1000 genomes]
rs3111554	0.93[ASN][1000 genomes]
rs4561584	0.93[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	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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2967505	KCNK6	cis	cerebellum	SCAN
rs2967505	ARHGEF1	cis	cerebellum	SCAN
rs2967505	PRR19	cis	cerebellum	SCAN
rs2967505	MRPS12	cis	parietal	SCAN
rs2967505	PPP1R14A	cis	cerebellum	SCAN
rs2967505	IL29	cis	parietal	SCAN
rs2967505	NFKBIB	cis	parietal	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36999200-37014400	ZNF genes & repeats	Adipose Nuclei	Adipose
2	chr19:36999200-37018000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr19:36999800-37017400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr19:37000000-37011600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
5	chr19:37000000-37016400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr19:37000000-37017000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
7	chr19:37000000-37017800	ZNF genes & repeats	Liver	Liver
8	chr19:37001000-37018000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
9	chr19:37001400-37010400	ZNF genes & repeats	Fetal Brain Male	brain
10	chr19:37001400-37010600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr19:37001400-37017200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr19:37001600-37016400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
13	chr19:37001600-37018200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr19:37002400-37005200	Weak transcription	Fetal Thymus	thymus
15	chr19:37002400-37009400	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr19:37002400-37010400	ZNF genes & repeats	Brain Hippocampus Middle	brain
17	chr19:37002400-37014000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr19:37002400-37014200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
19	chr19:37002600-37008200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr19:37002600-37010000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
21	chr19:37002600-37012400	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr19:37002600-37018000	ZNF genes & repeats	Fetal Brain Female	brain
23	chr19:37002800-37005400	Weak transcription	Lung	lung
24	chr19:37002800-37016400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr19:37002800-37016800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
26	chr19:37003200-37008800	ZNF genes & repeats	Brain Substantia Nigra	brain
27	chr19:37003200-37014400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
28	chr19:37003200-37014400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr19:37003200-37016800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr19:37003200-37017000	ZNF genes & repeats	Fetal Lung	lung
31	chr19:37003200-37018000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
32	chr19:37003400-37008800	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
33	chr19:37003400-37010400	ZNF genes & repeats	Fetal Kidney	kidney
34	chr19:37003400-37016800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
35	chr19:37003400-37017000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
36	chr19:37003400-37017200	ZNF genes & repeats	Dnd41	blood
37	chr19:37003400-37017400	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
38	chr19:37003600-37006200	ZNF genes & repeats	Psoas Muscle	Psoas
39	chr19:37003600-37006200	ZNF genes & repeats	Rectal Smooth Muscle	rectum
40	chr19:37003600-37006400	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
41	chr19:37003600-37006400	ZNF genes & repeats	Brain Angular Gyrus	brain
42	chr19:37003600-37008800	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
43	chr19:37003600-37009000	ZNF genes & repeats	HSMM	muscle
44	chr19:37003600-37010200	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
45	chr19:37003600-37010200	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
46	chr19:37003600-37010400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
47	chr19:37003600-37010400	ZNF genes & repeats	Stomach Smooth Muscle	stomach
48	chr19:37003600-37012200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
49	chr19:37003600-37012600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr19:37003600-37014400	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links