Variant report

Variant	rs709142
Chromosome Location	chr3:191118525-191118526
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 106 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10937477	1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs13061649	0.81[EUR][1000 genomes]
rs1347400	0.84[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs1465737	0.86[EUR][1000 genomes]
rs1473866	1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs150506	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs159488	0.87[ASN][1000 genomes]
rs159489	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1656143	0.82[EUR][1000 genomes]
rs1662184	0.81[EUR][1000 genomes]
rs167148	0.81[EUR][1000 genomes]
rs176820	0.82[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs176821	0.81[EUR][1000 genomes]
rs176822	0.81[EUR][1000 genomes]
rs184140	0.81[EUR][1000 genomes]
rs186063	0.92[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap];0.89[YRI][hapmap]
rs186064	0.81[EUR][1000 genomes]
rs186065	0.81[EUR][1000 genomes]
rs186066	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs188384	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs188385	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs192671	1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs211043	0.81[EUR][1000 genomes]
rs2572064	0.81[EUR][1000 genomes]
rs293797	1.00[CHB][hapmap];0.81[JPT][hapmap];0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs293798	1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs293800	0.91[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs293802	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs293804	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs293805	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs293806	0.82[CHB][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs293807	0.81[EUR][1000 genomes]
rs293808	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs293809	0.81[EUR][1000 genomes]
rs293810	0.81[EUR][1000 genomes]
rs293811	0.81[EUR][1000 genomes]
rs293812	0.81[EUR][1000 genomes]
rs293813	0.81[EUR][1000 genomes]
rs293814	0.81[EUR][1000 genomes]
rs293815	1.00[CHB][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs293837	0.82[EUR][1000 genomes]
rs293839	0.82[EUR][1000 genomes]
rs293840	0.82[EUR][1000 genomes]
rs293841	0.81[EUR][1000 genomes]
rs293844	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs293846	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs293851	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs297396	1.00[CHB][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs364519	0.81[EUR][1000 genomes]
rs366626	0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs367747	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs368665	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs369174	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs373035	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs381090	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs383075	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs383529	0.81[EUR][1000 genomes]
rs386241	0.82[EUR][1000 genomes]
rs389765	0.81[EUR][1000 genomes]
rs390744	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs392311	0.81[EUR][1000 genomes]
rs399575	0.82[EUR][1000 genomes]
rs401465	1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs403078	0.81[EUR][1000 genomes]
rs407226	0.81[EUR][1000 genomes]
rs415149	0.81[EUR][1000 genomes]
rs420266	0.81[EUR][1000 genomes]
rs426466	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs429374	0.81[EUR][1000 genomes]
rs429521	0.81[EUR][1000 genomes]
rs432085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs434556	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs436393	0.82[EUR][1000 genomes]
rs436428	0.82[EUR][1000 genomes]
rs437244	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs438589	0.82[EUR][1000 genomes]
rs441509	0.81[EUR][1000 genomes]
rs445914	0.81[EUR][1000 genomes]
rs447931	0.82[EUR][1000 genomes]
rs448133	1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs448643	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs449398	0.81[EUR][1000 genomes]
rs4677630	0.84[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs4677734	1.00[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs4677735	0.88[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs491252	0.81[EUR][1000 genomes]
rs513632	0.81[EUR][1000 genomes]
rs520494	0.82[EUR][1000 genomes]
rs520600	0.81[EUR][1000 genomes]
rs523270	1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs525774	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs526785	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs529523	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs566548	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs568702	0.81[EUR][1000 genomes]
rs578401	0.81[EUR][1000 genomes]
rs6779820	1.00[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs6953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs697905	0.82[CHB][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9847278	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931943	chr3:190860224-191321873	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2757910	chr3:190867011-191279107	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2759209	chr3:190867011-191279107	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv428428	chr3:190936834-191215596	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv998208	chr3:191021434-191175350	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv534269	chr3:191037181-191261730	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs709142	CCDC50	cis	Artery Tibial	GTEx
rs709142	CCDC50	cis	Artery Aorta	GTEx
rs709142	CCDC50	cis	Thyroid	GTEx

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:191079600-191121200	Weak transcription	Gastric	stomach
2	chr3:191080200-191118800	Weak transcription	Pancreas	Pancrea
3	chr3:191088600-191119600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:191093400-191119400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:191093400-191121400	Weak transcription	Esophagus	oesophagus
6	chr3:191096000-191130200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:191099400-191122000	Weak transcription	Fetal Brain Male	brain
8	chr3:191099600-191120000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr3:191100200-191119200	Weak transcription	Right Ventricle	heart
10	chr3:191100200-191119400	Weak transcription	Psoas Muscle	Psoas
11	chr3:191100200-191119600	Weak transcription	K562	blood
12	chr3:191100400-191120000	Weak transcription	Spleen	Spleen
13	chr3:191100400-191121600	Weak transcription	Fetal Brain Female	brain
14	chr3:191103200-191119400	Weak transcription	HSMMtube	muscle
15	chr3:191108600-191118800	Weak transcription	Brain Germinal Matrix	brain
16	chr3:191108800-191119400	Weak transcription	Aorta	Aorta
17	chr3:191110800-191119400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:191111000-191130400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:191114000-191121400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:191114200-191119200	Weak transcription	Fetal Intestine Large	intestine
21	chr3:191114200-191119400	Weak transcription	NHLF	lung
22	chr3:191114400-191119600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr3:191114400-191119600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr3:191114400-191120400	Weak transcription	HSMM	muscle
25	chr3:191114400-191121000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr3:191114400-191121400	Weak transcription	Brain Hippocampus Middle	brain
27	chr3:191116000-191119800	Weak transcription	Left Ventricle	heart
28	chr3:191116000-191119800	Weak transcription	Ovary	ovary
29	chr3:191116000-191121200	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr3:191116000-191121600	Weak transcription	Primary B cells from cord blood	blood
31	chr3:191116400-191118800	Weak transcription	Placenta	Placenta
32	chr3:191116600-191118800	Weak transcription	Osteobl	bone
33	chr3:191116600-191119600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr3:191116600-191119600	Weak transcription	Liver	Liver
35	chr3:191117000-191118600	Weak transcription	Primary B cells from peripheral blood	blood
36	chr3:191117000-191118600	Weak transcription	Stomach Smooth Muscle	stomach
37	chr3:191117200-191127200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:191117200-191127200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:191117800-191119600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:191118000-191119800	Weak transcription	Adipose Nuclei	Adipose
41	chr3:191118000-191121000	Weak transcription	HUVEC	blood vessel
42	chr3:191118200-191120000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr3:191118200-191127200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:191118400-191130000	Weak transcription	NH-A	brain

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