Variant report

Variant	rs6451339
Chromosome Location	chr5:37696178-37696179
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:113)

rs_ID	r²[population]
rs10062316	0.82[CHB][hapmap]
rs1013398	0.82[CHB][hapmap]
rs1019505	0.91[MEX][hapmap]
rs10805627	0.91[ASN][1000 genomes]
rs10941344	0.82[CHB][hapmap]
rs10941345	0.83[CHB][hapmap]
rs10941347	0.83[CHB][hapmap]
rs10941348	0.83[CHB][hapmap]
rs10941351	0.83[CHB][hapmap]
rs10941352	0.82[CHB][hapmap]
rs10941353	0.83[CHB][hapmap]
rs10941356	0.83[CHB][hapmap]
rs10941358	0.89[ASN][1000 genomes]
rs10941359	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs11739400	0.96[ASN][1000 genomes]
rs11740897	0.91[ASN][1000 genomes]
rs11742904	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs11745953	1.00[CEU][hapmap];0.81[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11745980	0.96[ASN][1000 genomes]
rs11747548	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11747900	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs11749563	0.88[ASN][1000 genomes]
rs11750837	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11750840	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11949124	0.83[CHB][hapmap]
rs11950295	0.83[CHB][hapmap]
rs11954727	0.82[CHB][hapmap]
rs11957813	0.82[CHB][hapmap]
rs12152831	0.83[CHB][hapmap]
rs12188864	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12189078	1.00[CEU][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12332088	0.92[ASN][1000 genomes]
rs12516955	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs12520944	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12521063	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12654893	0.83[CHB][hapmap]
rs12655908	0.89[ASW][hapmap];0.83[CHB][hapmap]
rs1356433	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1400851	0.83[CHB][hapmap]
rs1400854	0.89[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.96[ASN][1000 genomes]
rs1517785	0.83[CHB][hapmap]
rs1517786	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs1589116	0.82[CHB][hapmap]
rs1589119	0.91[ASN][1000 genomes]
rs1996427	0.94[ASN][1000 genomes]
rs2088077	0.83[CHB][hapmap]
rs2101786	0.83[CHB][hapmap]
rs2176479	0.91[ASN][1000 genomes]
rs2366673	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4242251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4257799	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4343860	0.89[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.98[ASN][1000 genomes]
rs4357062	0.83[CHB][hapmap]
rs4371784	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4451075	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4482927	0.98[ASN][1000 genomes]
rs4516881	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4516882	0.99[ASN][1000 genomes]
rs4541680	0.87[ASN][1000 genomes]
rs4582305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4594879	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4608942	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4618454	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4869438	0.83[CHB][hapmap]
rs4869439	0.83[CHB][hapmap]
rs4869440	0.83[CHB][hapmap]
rs4869530	0.89[ASW][hapmap];0.83[CHB][hapmap]
rs4869535	0.83[CHB][hapmap]
rs4869538	0.83[CHB][hapmap]
rs4869541	0.96[ASN][1000 genomes]
rs4869543	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55708822	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55732996	0.90[ASN][1000 genomes]
rs55742744	0.90[ASN][1000 genomes]
rs55849485	0.92[ASN][1000 genomes]
rs56007806	0.93[ASN][1000 genomes]
rs56051431	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56051756	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56100322	0.90[ASN][1000 genomes]
rs56412589	0.91[ASN][1000 genomes]
rs56832651	0.94[ASN][1000 genomes]
rs59378089	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59409868	0.94[ASN][1000 genomes]
rs59829323	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60589722	0.90[ASN][1000 genomes]
rs61492379	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62358883	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62360907	0.91[ASN][1000 genomes]
rs62360910	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6451329	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs6451330	0.89[ASN][1000 genomes]
rs6451331	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs6451333	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs6451337	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6863936	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs6864924	0.84[ASN][1000 genomes]
rs6868428	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs6874891	0.83[CHB][hapmap]
rs6884551	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6884569	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6885057	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs6885329	0.91[ASN][1000 genomes]
rs6887215	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6887613	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs6889616	0.82[CHB][hapmap]
rs72743184	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7702644	0.91[ASN][1000 genomes]
rs7703775	0.91[ASN][1000 genomes]
rs7713017	0.83[CHB][hapmap]
rs7718557	0.82[CHB][hapmap]
rs7725465	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7727807	0.80[CHB][hapmap]
rs9292656	0.82[CHB][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	nsv1026554	chr5:37112133-37734859	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv537726	chr5:37112133-37734859	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
3	nsv949716	chr5:37179341-37967352	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
4	nsv1023871	chr5:37330018-37804744	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv537729	chr5:37330018-37804744	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv432744	chr5:37374124-37743077	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv597846	chr5:37430215-37813591	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1030250	chr5:37478163-37734859	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv881383	chr5:37485316-37773877	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6451339	WDR70	cis	lymphoblastoid	seeQTL
rs6451339	LIFR	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:37682200-37698000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr5:37683800-37696600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr5:37684400-37700000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr5:37684400-37705000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr5:37685200-37696600	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr5:37685200-37743200	Weak transcription	Gastric	stomach
7	chr5:37685400-37717600	Weak transcription	Pancreas	Pancrea
8	chr5:37685600-37711200	Weak transcription	Fetal Stomach	stomach
9	chr5:37685600-37727000	Weak transcription	Lung	lung
10	chr5:37687200-37720600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr5:37688400-37721400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr5:37688400-37721400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr5:37688400-37723600	Weak transcription	Placenta	Placenta
14	chr5:37689600-37696600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr5:37689600-37726000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr5:37692200-37721200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr5:37693800-37705200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr5:37694600-37698400	Weak transcription	Dnd41	blood
19	chr5:37694800-37698400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr5:37694800-37698400	Weak transcription	Adipose Nuclei	Adipose
21	chr5:37695200-37716600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr5:37695400-37696800	Enhancers	Psoas Muscle	Psoas
23	chr5:37695400-37698000	Weak transcription	Monocytes-CD14+_RO01746	blood
24	chr5:37695400-37698400	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr5:37695400-37706000	Weak transcription	Stomach Smooth Muscle	stomach
26	chr5:37695400-37715600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr5:37695400-37722600	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr5:37695600-37697400	Enhancers	Hela-S3	cervix
29	chr5:37695600-37697400	Enhancers	HMEC	breast
30	chr5:37695600-37698200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr5:37695600-37698400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr5:37695600-37702000	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr5:37695600-37703000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr5:37695600-37706400	Weak transcription	Liver	Liver
35	chr5:37695600-37721200	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr5:37695800-37696600	Weak transcription	Primary T cells from cord blood	blood
37	chr5:37695800-37696800	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr5:37695800-37697200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr5:37695800-37697400	Enhancers	NHEK	skin
40	chr5:37695800-37705200	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr5:37696000-37696400	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr5:37696000-37696800	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr5:37696000-37697200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr5:37696000-37697400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr5:37696000-37697400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr5:37696000-37697400	Enhancers	NHDF-Ad	bronchial
47	chr5:37696000-37697600	Weak transcription	Primary T helper cells fromperipheralblood	blood
48	chr5:37696000-37717000	Weak transcription	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links