Variant report

Variant	rs293809
Chromosome Location	chr3:191097391-191097392
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:191096520..191099526-chr3:191099935..191102784,3	K562	blood:
2	chr3:191094269..191095897-chr3:191095965..191098815,2	MCF-7	breast:

Extended variants
information (count: 99 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1066857	0.96[ASN][1000 genomes]
rs13061649	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs150505	0.95[ASN][1000 genomes]
rs1520200	0.86[CHB][hapmap]
rs1656143	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1662184	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs167148	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1715641	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs176821	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs176822	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs184140	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1850961	0.89[ASN][1000 genomes]
rs186064	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs186065	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs186066	0.82[EUR][1000 genomes]
rs186068	0.94[ASN][1000 genomes]
rs188384	0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs211043	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2572064	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs293800	0.91[YRI][hapmap];0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs293802	0.86[YRI][hapmap];0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs293804	0.81[EUR][1000 genomes]
rs293805	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs293806	0.90[LWK][hapmap];0.85[MKK][hapmap];0.89[TSI][hapmap];0.93[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs293807	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs293808	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs293810	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs293811	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs293812	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs293813	0.92[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs293814	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs293816	0.90[ASN][1000 genomes]
rs293817	0.90[ASN][1000 genomes]
rs293837	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs293839	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs293840	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs293841	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs293852	0.97[ASN][1000 genomes]
rs293854	0.97[ASN][1000 genomes]
rs293856	0.97[ASN][1000 genomes]
rs293857	0.97[ASN][1000 genomes]
rs293858	0.97[ASN][1000 genomes]
rs293859	0.95[ASN][1000 genomes]
rs293861	0.95[ASN][1000 genomes]
rs364519	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs367747	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs368665	0.82[EUR][1000 genomes]
rs369174	1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs381090	0.80[EUR][1000 genomes]
rs383075	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs383529	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs386241	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs389765	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs390744	0.93[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs392311	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs399575	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs403078	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs407226	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs415149	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs420266	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs423989	0.95[ASN][1000 genomes]
rs429374	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs429521	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs432085	0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs434556	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs436393	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs436428	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs437244	0.81[EUR][1000 genomes]
rs438589	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs440266	0.95[ASN][1000 genomes]
rs441509	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs445914	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs447931	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs449398	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4677735	0.81[TSI][hapmap]
rs491252	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs497918	0.93[ASN][1000 genomes]
rs513632	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs520494	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs520600	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs529523	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs566548	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs568702	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs578401	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6953	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs695910	0.89[ASN][1000 genomes]
rs696347	0.95[ASN][1000 genomes]
rs696348	0.95[ASN][1000 genomes]
rs696349	0.95[ASN][1000 genomes]
rs697905	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs697913	0.93[ASN][1000 genomes]
rs709142	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	nsv878107	chr3:191069984-191100073	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs293809	CCDC50	cis	Artery Aorta	GTEx
rs293809	CCDC50	cis	Thyroid	GTEx
rs293809	CCDC50	cis	Artery Tibial	GTEx

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:191071200-191114000	Weak transcription	Colonic Mucosa	Colon
2	chr3:191071400-191097400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr3:191071400-191100000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:191072600-191100800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:191075000-191097400	Weak transcription	Thymus	Thymus
6	chr3:191079400-191115800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:191079600-191099200	Weak transcription	Spleen	Spleen
8	chr3:191079600-191116400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:191079600-191121200	Weak transcription	Gastric	stomach
10	chr3:191080200-191110200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr3:191080200-191118800	Weak transcription	Pancreas	Pancrea
12	chr3:191080600-191110400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr3:191087000-191115400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr3:191087800-191100000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr3:191087800-191109200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:191088000-191109800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr3:191088600-191119600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:191093400-191097400	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr3:191093400-191097400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr3:191093400-191097400	Weak transcription	HepG2	liver
21	chr3:191093400-191097600	Weak transcription	Fetal Muscle Trunk	muscle
22	chr3:191093400-191098200	Weak transcription	Left Ventricle	heart
23	chr3:191093400-191099200	Weak transcription	Aorta	Aorta
24	chr3:191093400-191099200	Weak transcription	Lung	lung
25	chr3:191093400-191119400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr3:191093400-191121400	Weak transcription	Esophagus	oesophagus
27	chr3:191093600-191098000	Weak transcription	Duodenum Mucosa	Duodenum
28	chr3:191093600-191098400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr3:191093800-191097600	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr3:191093800-191097800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr3:191093800-191098200	Weak transcription	Stomach Smooth Muscle	stomach
32	chr3:191094000-191098800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr3:191094200-191097400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr3:191094400-191098000	Weak transcription	Brain Germinal Matrix	brain
35	chr3:191094400-191098200	Weak transcription	Fetal Intestine Large	intestine
36	chr3:191094400-191098400	Weak transcription	Fetal Brain Female	brain
37	chr3:191094600-191098200	Weak transcription	Fetal Stomach	stomach
38	chr3:191094600-191100600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr3:191094800-191097400	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr3:191094800-191097400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr3:191094800-191097400	Weak transcription	Liver	Liver
42	chr3:191094800-191098000	Enhancers	Adipose Nuclei	Adipose
43	chr3:191094800-191098000	Enhancers	Fetal Lung	lung
44	chr3:191094800-191098200	Weak transcription	Brain Anterior Caudate	brain
45	chr3:191094800-191102200	Weak transcription	Brain Cingulate Gyrus	brain
46	chr3:191094800-191114800	Weak transcription	A549	lung
47	chr3:191095000-191097400	Enhancers	HSMMtube	muscle
48	chr3:191095000-191097600	Weak transcription	NHEK	skin
49	chr3:191095000-191098000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr3:191095000-191098400	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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