Variant report

Variant	rs10873951
Chromosome Location	chr1:78075766-78075767
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 122 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs1013399	0.81[ASN][1000 genomes]
rs10782654	0.85[ASN][1000 genomes]
rs10873949	0.85[ASN][1000 genomes]
rs10873950	1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs11162362	0.85[ASN][1000 genomes]
rs11162364	0.86[ASN][1000 genomes]
rs11162365	0.92[ASN][1000 genomes]
rs11162368	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11162369	0.99[ASN][1000 genomes]
rs11162370	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs11162372	0.98[ASN][1000 genomes]
rs11162374	0.83[EUR][1000 genomes]
rs11162378	0.81[CEU][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs1166586	0.84[CEU][hapmap]
rs1166588	0.89[JPT][hapmap]
rs12071212	0.82[ASN][1000 genomes]
rs12074409	1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs12095064	0.82[ASN][1000 genomes]
rs12128041	1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap]
rs12132838	0.85[CEU][hapmap]
rs12135104	0.81[EUR][1000 genomes]
rs12142441	0.85[CEU][hapmap];0.86[TSI][hapmap]
rs12142671	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12717767	0.92[ASN][1000 genomes]
rs12717768	0.85[EUR][1000 genomes]
rs12724560	0.85[ASN][1000 genomes]
rs1389789	0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs1389790	0.85[CEU][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs1539739	0.81[CEU][hapmap];0.84[TSI][hapmap]
rs1565850	1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs1565851	1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs1565852	0.89[ASN][1000 genomes]
rs166770	0.85[CEU][hapmap];0.85[EUR][1000 genomes]
rs1962523	1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs2029768	0.94[CHB][hapmap];0.94[CHD][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs2031342	0.85[CEU][hapmap];0.86[TSI][hapmap]
rs203229	0.85[CEU][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs2147318	0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs2172727	1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.86[ASN][1000 genomes]
rs2274123	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs2296227	0.85[CEU][hapmap];0.89[TSI][hapmap]
rs2647486	0.94[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs2647487	0.81[ASN][1000 genomes]
rs278834	0.84[EUR][1000 genomes]
rs278837	0.84[CEU][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs278838	0.87[ASN][1000 genomes]
rs278841	0.81[EUR][1000 genomes]
rs278842	0.85[CEU][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs278845	0.92[ASN][1000 genomes]
rs278847	0.93[ASN][1000 genomes]
rs278848	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs278850	0.85[CEU][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs278851	0.83[EUR][1000 genomes]
rs278852	0.90[ASN][1000 genomes]
rs278854	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs278855	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs278856	0.83[EUR][1000 genomes]
rs278860	0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs278862	0.94[ASN][1000 genomes]
rs278863	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs2803136	0.89[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap]
rs2803168	0.94[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs3509	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs371076	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3738079	0.82[ASN][1000 genomes]
rs3767030	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap]
rs3767032	0.81[ASN][1000 genomes]
rs3767033	0.81[ASN][1000 genomes]
rs3767037	0.85[CEU][hapmap];0.89[TSI][hapmap]
rs3767038	0.85[CEU][hapmap];0.86[TSI][hapmap]
rs4245658	1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs4589153	1.00[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs4600093	1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs4949658	0.94[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs4949659	0.94[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs4949807	0.84[ASN][1000 genomes]
rs4949808	0.85[ASN][1000 genomes]
rs4949809	1.00[CHB][hapmap];0.83[JPT][hapmap];0.87[ASN][1000 genomes]
rs4949811	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs4949813	0.91[ASN][1000 genomes]
rs4949816	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4949817	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs4949818	0.85[CEU][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs574973	0.85[CEU][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs6603953	0.81[ASN][1000 genomes]
rs6603955	0.92[ASN][1000 genomes]
rs6603958	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs6603960	0.85[CEU][hapmap]
rs6661656	0.85[CEU][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs6667519	1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs6667803	1.00[CHB][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs6675743	1.00[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs6687501	0.85[CEU][hapmap];0.89[TSI][hapmap]
rs6692369	0.84[ASN][1000 genomes]
rs6693100	0.85[ASN][1000 genomes]
rs6695989	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs6696083	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs6699205	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs6699311	0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs717333	0.85[CEU][hapmap];0.89[TSI][hapmap]
rs728741	1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.80[LWK][hapmap];0.91[ASN][1000 genomes]
rs7513619	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7519476	0.85[ASN][1000 genomes]
rs7521042	0.86[ASN][1000 genomes]
rs7524147	0.84[ASN][1000 genomes]
rs7524866	0.94[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs7531286	0.89[CHB][hapmap]
rs7535781	0.85[CEU][hapmap];0.87[TSI][hapmap]
rs7545544	0.94[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs7546365	0.85[CEU][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs7551211	0.94[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs7551729	0.94[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs7556523	0.85[EUR][1000 genomes]
rs8179272	0.85[CEU][hapmap];0.86[TSI][hapmap]
rs872342	0.85[CEU][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs962388	0.91[ASN][1000 genomes]
rs9787153	0.82[ASN][1000 genomes]
rs9988619	0.85[EUR][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	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv870709	chr1:78016517-78198322	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	esv3337461	chr1:78036000-78153859	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10873951	AK5	cis	parietal	SCAN
rs10873951	USP33	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78047600-78085600	Weak transcription	NHLF	lung
2	chr1:78047800-78086200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr1:78047800-78090000	Weak transcription	NH-A	brain
4	chr1:78048000-78077800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:78048000-78097400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:78059000-78083200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:78063200-78083000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:78063600-78097600	Weak transcription	Fetal Brain Male	brain
9	chr1:78070600-78098000	Weak transcription	Rectal Smooth Muscle	rectum
10	chr1:78071000-78098000	Weak transcription	Colonic Mucosa	Colon
11	chr1:78071200-78085600	Weak transcription	HUVEC	blood vessel
12	chr1:78071200-78098000	Weak transcription	Small Intestine	intestine
13	chr1:78071400-78097800	Weak transcription	Aorta	Aorta
14	chr1:78071800-78082800	Weak transcription	Osteobl	bone
15	chr1:78071800-78097800	Weak transcription	Ovary	ovary
16	chr1:78071800-78097800	Weak transcription	Pancreas	Pancrea
17	chr1:78072000-78080600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:78072000-78094600	Weak transcription	Left Ventricle	heart
19	chr1:78072000-78097600	Weak transcription	Gastric	stomach
20	chr1:78072200-78083400	Weak transcription	Thymus	Thymus
21	chr1:78072200-78086400	Weak transcription	HMEC	breast
22	chr1:78072200-78090600	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr1:78072200-78098000	Weak transcription	Spleen	Spleen
24	chr1:78072400-78087200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:78072400-78097800	Weak transcription	Lung	lung
26	chr1:78072600-78080600	Weak transcription	HSMM	muscle
27	chr1:78072600-78086200	Weak transcription	Fetal Thymus	thymus
28	chr1:78072600-78097800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr1:78072800-78086400	Weak transcription	Fetal Kidney	kidney
30	chr1:78073000-78090000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:78073200-78097400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr1:78073600-78076000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr1:78073600-78076400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr1:78073600-78082200	Weak transcription	Fetal Intestine Small	intestine
35	chr1:78073600-78086800	Weak transcription	Fetal Stomach	stomach
36	chr1:78073800-78076600	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr1:78073800-78078200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr1:78074000-78076000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
39	chr1:78074000-78076600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr1:78074000-78077400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr1:78074200-78076400	ZNF genes & repeats	Primary B cells from cord blood	blood
42	chr1:78074200-78076600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr1:78074400-78076600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
44	chr1:78074400-78076600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
45	chr1:78074400-78086200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr1:78074600-78076600	ZNF genes & repeats	Primary T cells from cord blood	blood
47	chr1:78074600-78077400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
48	chr1:78074600-78092000	Weak transcription	Fetal Heart	heart
49	chr1:78074800-78076400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
50	chr1:78074800-78076800	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links