Variant report

Variant	rs11985628
Chromosome Location	chr8:66542739-66542740
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:66542582..66544230-chr8:66545010..66546585,2	MCF-7	breast:
2	chr8:66541684..66544207-chr8:66544873..66547787,2	K562	blood:

Variant related genes	Relation type
ENSG00000104442	Chromatin interaction

Extended variants
information (count: 120 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs10087361	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10089029	1.00[ASN][1000 genomes]
rs10089708	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10092109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10097461	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10100131	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10110985	0.83[ASN][1000 genomes]
rs1053085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1053087	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1053088	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10957361	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11776709	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11776712	0.91[ASN][1000 genomes]
rs11990855	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12335006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12335276	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12543053	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12544767	0.95[ASN][1000 genomes]
rs12677419	0.98[ASN][1000 genomes]
rs12678467	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs13252358	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13266834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13267942	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13268343	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap]
rs13281155	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs14213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1473601	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1533285	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16932245	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16932250	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16932314	0.94[ASN][1000 genomes]
rs1877638	0.95[ASN][1000 genomes]
rs2048650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2102648	0.97[ASN][1000 genomes]
rs2175809	0.98[ASN][1000 genomes]
rs2175810	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2357476	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28415299	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28576524	0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs28613797	1.00[ASN][1000 genomes]
rs3268	0.99[ASN][1000 genomes]
rs34226237	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34494846	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34533611	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34851482	0.98[ASN][1000 genomes]
rs35038843	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35790435	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35941313	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3750184	0.99[ASN][1000 genomes]
rs3765205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3812412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4275254	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4320587	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4384016	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4384017	0.84[ASN][1000 genomes]
rs4388482	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4397444	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4637885	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4637886	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4737222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4737747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4737748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4737749	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4737750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5018458	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57419568	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60023200	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60058315	0.99[ASN][1000 genomes]
rs6472210	0.92[CHB][hapmap];0.83[JPT][hapmap]
rs6472213	0.99[ASN][1000 genomes]
rs6472214	0.88[ASN][1000 genomes]
rs6472215	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6472216	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6472217	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6472218	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66467166	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs66486920	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67046768	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67131486	0.95[ASN][1000 genomes]
rs67685675	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6985897	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6985932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6986445	0.82[AMR][1000 genomes]
rs6986691	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6986866	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6991731	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6993876	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6994213	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6995242	0.99[ASN][1000 genomes]
rs6997959	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7006261	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7006648	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7007505	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7011464	0.88[CHB][hapmap]
rs7012578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7012856	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7016472	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs71930161	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73236948	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73236986	1.00[ASN][1000 genomes]
rs73239011	1.00[ASN][1000 genomes]
rs73239085	0.99[ASN][1000 genomes]
rs7459737	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7464123	0.92[ASN][1000 genomes]
rs7464223	0.95[ASN][1000 genomes]
rs7812390	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7812446	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7814841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7815488	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7817112	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7823840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7832407	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7835313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7836349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7836746	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7841652	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7842162	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7846527	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs953593	0.87[CHB][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761434	chr8:65578467-66567678	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11985628	CTD-3025N20.3	cis	Esophagus Muscularis	GTEx
rs11985628	CTD-3025N20.3	cis	Esophagus Mucosa	GTEx
rs11985628	CTD-3025N20.3	cis	lung	GTEx
rs11985628	CTD-3025N20.3	cis	Artery Tibial	GTEx
rs11985628	CTD-3025N20.3	cis	Muscle Skeletal	GTEx
rs11985628	CTD-3025N20.3	cis	Thyroid	GTEx
rs11985628	ARMC1	cis	multi-tissue	Pritchard

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:66504000-66545200	Weak transcription	Fetal Brain Male	brain
2	chr8:66506800-66545200	Weak transcription	Stomach Mucosa	stomach
3	chr8:66508000-66545200	Weak transcription	Fetal Heart	heart
4	chr8:66518000-66545600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr8:66519600-66545200	Weak transcription	Right Atrium	heart
6	chr8:66520000-66545000	Weak transcription	NHEK	skin
7	chr8:66522600-66545200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr8:66525600-66545200	Weak transcription	Fetal Kidney	kidney
9	chr8:66530200-66545000	Weak transcription	Hela-S3	cervix
10	chr8:66532000-66545600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr8:66532400-66545600	Weak transcription	Aorta	Aorta
12	chr8:66533600-66545200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr8:66534000-66545200	Weak transcription	Brain Angular Gyrus	brain
14	chr8:66534200-66545200	Weak transcription	Colonic Mucosa	Colon
15	chr8:66534400-66545200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr8:66534600-66545200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr8:66535000-66544800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr8:66535000-66545200	Weak transcription	Brain Hippocampus Middle	brain
19	chr8:66535200-66545200	Weak transcription	Esophagus	oesophagus
20	chr8:66535200-66545600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr8:66536400-66543200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr8:66537600-66545200	Weak transcription	Gastric	stomach
23	chr8:66537800-66544800	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr8:66537800-66545000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr8:66538000-66543800	Weak transcription	HSMM	muscle
26	chr8:66538000-66545200	Weak transcription	Colon Smooth Muscle	Colon
27	chr8:66538000-66545200	Weak transcription	NH-A	brain
28	chr8:66538200-66545000	Weak transcription	A549	lung
29	chr8:66538600-66545000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr8:66539000-66544800	Weak transcription	HMEC	breast
31	chr8:66539200-66545000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr8:66539200-66545000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr8:66539200-66545000	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr8:66539200-66545200	Weak transcription	Rectal Smooth Muscle	rectum
35	chr8:66539400-66544800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr8:66539400-66545000	Weak transcription	Fetal Lung	lung
37	chr8:66539400-66545200	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr8:66539400-66545200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr8:66539600-66543400	Weak transcription	Fetal Stomach	stomach
40	chr8:66539600-66544400	Weak transcription	Brain Cingulate Gyrus	brain
41	chr8:66539600-66544400	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr8:66539600-66544600	Weak transcription	Primary B cells from cord blood	blood
43	chr8:66539600-66544600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr8:66539600-66544800	Weak transcription	Brain Germinal Matrix	brain
45	chr8:66539600-66544800	Weak transcription	Fetal Intestine Large	intestine
46	chr8:66539600-66544800	Weak transcription	Lung	lung
47	chr8:66539600-66544800	Weak transcription	Psoas Muscle	Psoas
48	chr8:66539600-66545000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr8:66539600-66545000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr8:66539600-66545000	Weak transcription	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links