Variant report

Variant	rs1474640
Chromosome Location	chr6:149813940-149813941
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 98 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10485097	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10782310	0.81[CHB][hapmap]
rs10782312	0.81[CHB][hapmap]
rs11155662	0.81[CHB][hapmap]
rs11155670	0.81[CHB][hapmap]
rs11155671	0.81[CHB][hapmap]
rs1125107	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12234128	0.81[CHB][hapmap]
rs12524946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12529698	0.81[CHB][hapmap]
rs12663698	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12665533	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17732745	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2064520	0.81[CHB][hapmap]
rs2105200	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2341550	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2341551	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2341768	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28580659	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2880075	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34870994	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3734295	0.81[CHB][hapmap]
rs3777949	0.81[CHB][hapmap]
rs3798761	0.81[CHB][hapmap]
rs3813675	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3924871	0.81[CHB][hapmap]
rs4869797	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4897128	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4897130	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4897131	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4897132	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4897133	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4897137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4897138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4897139	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60404985	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62439778	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62442787	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62442788	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62442789	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62442790	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62442792	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62442793	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62442795	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62442798	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6570968	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6911016	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6929614	0.98[ASN][1000 genomes]
rs761617	0.88[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7740278	0.81[CHB][hapmap]
rs7753560	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7767622	0.81[CHB][hapmap]
rs7774559	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7774597	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs909792	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9285521	0.81[CHB][hapmap]
rs9322184	0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9322185	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9322188	0.80[CHB][hapmap]
rs9322198	0.81[CHB][hapmap]
rs9322200	0.80[CHB][hapmap]
rs9322209	0.81[CHB][hapmap]
rs9373594	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9373595	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9373596	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9377220	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9377221	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9377223	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9377224	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9377230	0.81[CHB][hapmap]
rs9390684	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9390687	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9390688	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9390689	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9393175	0.80[CHB][hapmap]
rs9399689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9399690	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9404042	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9404043	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9404044	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9404048	0.81[CHB][hapmap]
rs9406344	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9498368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9689569	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9689723	0.81[CHB][hapmap]
rs9718079	0.81[CHB][hapmap]
rs9767105	0.81[CHB][hapmap]
rs9767123	0.81[CHB][hapmap]
rs9767555	0.81[CHB][hapmap]
rs9767713	0.81[CHB][hapmap]
rs9800580	0.81[CHB][hapmap]
rs9800614	0.81[CHB][hapmap]
rs9800648	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9800686	0.81[CHB][hapmap]
rs9800736	0.81[CHB][hapmap]
rs9968911	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530444	chr6:149654540-149848997	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv1832313	chr6:149789511-149840750	Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1474640	RP11-350J20.5	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149804400-149824600	Weak transcription	Brain Hippocampus Middle	brain
2	chr6:149806400-149832000	Weak transcription	HSMMtube	muscle
3	chr6:149806400-149844800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr6:149806800-149825200	Weak transcription	HSMM	muscle
5	chr6:149806800-149832400	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr6:149807000-149814000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr6:149807000-149814600	Weak transcription	Fetal Thymus	thymus
8	chr6:149807000-149832200	Weak transcription	Lung	lung
9	chr6:149807000-149849000	Weak transcription	Gastric	stomach
10	chr6:149807200-149815600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr6:149807200-149824800	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr6:149807200-149832000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr6:149807200-149835000	Weak transcription	Spleen	Spleen
14	chr6:149807200-149842600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr6:149808000-149814000	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr6:149810200-149814200	Weak transcription	Stomach Mucosa	stomach
17	chr6:149810200-149819800	Weak transcription	Fetal Muscle Trunk	muscle
18	chr6:149810400-149814200	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr6:149810400-149821200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr6:149810600-149814000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr6:149810800-149814000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr6:149810800-149851600	Weak transcription	Esophagus	oesophagus
23	chr6:149811200-149814000	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr6:149811200-149814400	Weak transcription	HepG2	liver
25	chr6:149811200-149860600	Weak transcription	Aorta	Aorta
26	chr6:149811400-149814000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr6:149811400-149826600	Weak transcription	Fetal Intestine Small	intestine
28	chr6:149811600-149814000	Weak transcription	Primary B cells from cord blood	blood
29	chr6:149812200-149814000	Weak transcription	Primary B cells from peripheral blood	blood
30	chr6:149812400-149814000	Weak transcription	GM12878-XiMat	blood
31	chr6:149813000-149814000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr6:149813200-149818000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr6:149813800-149816200	Enhancers	Primary T cells fromperipheralblood	blood
34	chr6:149813800-149816400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr6:149813800-149817000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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