Variant report

Variant	rs952837
Chromosome Location	chr1:86172978-86172979
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:86043660..86051626-chr1:86167839..86177430,17	K562	blood:
2	chr1:86046116..86050935-chr1:86168336..86177340,12	K562	blood:
3	chr1:86048055..86050244-chr1:86170828..86173299,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272691	Chromatin interaction
ENSG00000142871	Chromatin interaction
ENSG00000153904	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1047892	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1047893	0.92[CEU][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs1047895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10518350	0.83[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs10782553	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs10873710	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs10873716	0.83[CEU][hapmap]
rs10873717	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1094359	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11161643	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11161645	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11161651	0.83[CEU][hapmap]
rs11161654	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11161657	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11161658	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11161661	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11161663	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11161665	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11161667	0.83[EUR][1000 genomes]
rs11578464	0.93[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs12063702	0.84[EUR][1000 genomes]
rs12089500	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12128916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12566746	0.89[CEU][hapmap];0.83[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12752817	0.84[EUR][1000 genomes]
rs1539444	0.93[CEU][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1764285	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1764288	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1764289	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1764291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1764292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1764299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1775988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1775990	0.96[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs184340	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1889919	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1889920	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1928626	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2389970	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2785081	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2995537	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs313727	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs313729	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34448540	0.81[ASN][1000 genomes]
rs373787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3753786	0.93[CEU][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3753789	0.85[CEU][hapmap]
rs3753790	0.83[CEU][hapmap]
rs3767162	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs414618	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs418979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs419409	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs424205	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs434853	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs447446	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs450145	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4912441	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4949915	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs61783617	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6667094	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6672312	0.93[CEU][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6689168	0.84[CEU][hapmap]
rs6689925	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6697535	0.90[CEU][hapmap];0.83[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6699497	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs709801	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7520491	0.89[CEU][hapmap]
rs7532758	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7554844	0.85[EUR][1000 genomes]
rs821379	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs821381	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs821386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs821389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs821391	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs821393	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs821394	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs821395	0.84[AFR][1000 genomes]
rs821396	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs821401	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs843969	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9324154	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9700177	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv3391173	chr1:86005637-86337469	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv817212	chr1:86127851-86658426	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv871471	chr1:86143084-86211516	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs952837	ZNHIT6	cis	Esophagus Muscularis	GTEx
rs952837	ZNHIT6	cis	Adipose Subcutaneous	GTEx
rs952837	ZNHIT6	cis	Artery Aorta	GTEx
rs952837	C1orf181	Cis_1M	lymphoblastoid	RTeQTL
rs952837	ZNHIT6	cis	lung	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86103400-86173000	Weak transcription	Pancreas	Pancrea
2	chr1:86157800-86173000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:86158000-86173000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:86167800-86173000	Weak transcription	Lung	lung
5	chr1:86170600-86173000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:86171200-86173000	Weak transcription	Esophagus	oesophagus
7	chr1:86171400-86173000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:86171600-86173000	Weak transcription	Left Ventricle	heart
9	chr1:86171600-86174600	Active TSS	GM12878-XiMat	blood
10	chr1:86171800-86173000	Weak transcription	Fetal Muscle Trunk	muscle
11	chr1:86171800-86173800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:86172000-86173000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:86172000-86173000	Weak transcription	Placenta	Placenta
14	chr1:86172000-86173400	Flanking Active TSS	Primary hematopoietic stem cells	blood
15	chr1:86172000-86174800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:86172200-86173000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:86172200-86173000	Flanking Active TSS	Fetal Kidney	kidney
18	chr1:86172200-86173000	Flanking Active TSS	NHEK	skin
19	chr1:86172200-86173000	Flanking Active TSS	Osteobl	bone
20	chr1:86172200-86173200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:86172200-86174600	Active TSS	K562	blood
22	chr1:86172200-86174600	Active TSS	NHLF	lung
23	chr1:86172400-86173000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:86172400-86173000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr1:86172400-86173000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr1:86172400-86173000	Enhancers	Placenta Amnion	Placenta Amnion
27	chr1:86172400-86173000	Enhancers	Stomach Mucosa	stomach
28	chr1:86172400-86173200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
29	chr1:86172400-86173400	Flanking Active TSS	Primary B cells from cord blood	blood
30	chr1:86172400-86173400	Flanking Active TSS	Primary T cells from cord blood	blood
31	chr1:86172400-86173400	Flanking Active TSS	Brain Cingulate Gyrus	brain
32	chr1:86172400-86173400	Flanking Active TSS	Dnd41	blood
33	chr1:86172400-86173600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:86172400-86173600	Flanking Active TSS	HUVEC	blood vessel
35	chr1:86172400-86173600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr1:86172400-86174000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr1:86172400-86174600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:86172400-86174800	Active TSS	HUES6 Cell Line	embryonic stem cell
39	chr1:86172400-86174800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:86172400-86175000	Active TSS	A549	lung
41	chr1:86172600-86173000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr1:86172600-86173000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr1:86172600-86173000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
44	chr1:86172600-86173000	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr1:86172600-86173000	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr1:86172600-86173000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr1:86172600-86173000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr1:86172600-86173000	Flanking Active TSS	Colon Smooth Muscle	Colon
49	chr1:86172600-86173000	Enhancers	Gastric	stomach
50	chr1:86172600-86173000	Active TSS	Psoas Muscle	Psoas

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links