Variant report

Variant	rs829646
Chromosome Location	chr2:30719326-30719327
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:30716986..30719566-chr2:30719646..30721612,2	MCF-7	breast:
2	chr2:30669035..30670943-chr2:30718081..30720596,2	MCF-7	breast:
3	chr2:30707407..30710110-chr2:30718002..30720308,3	K562	blood:

Variant related genes	Relation type
ENSG00000172954	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10167083	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs10175399	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10183928	0.85[CEU][hapmap];0.85[JPT][hapmap]
rs12053428	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs12468064	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs1252624	0.83[EUR][1000 genomes]
rs1252625	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs1252631	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs1252646	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1252651	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs1252654	1.00[JPT][hapmap]
rs1525062	0.86[CEU][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap]
rs17009706	0.86[YRI][hapmap]
rs1869423	0.86[CEU][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap]
rs1869424	0.86[CEU][hapmap];0.95[GIH][hapmap];0.81[TSI][hapmap]
rs1975555	0.86[CEU][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap]
rs2121600	0.86[CEU][hapmap]
rs2123753	0.86[CEU][hapmap];0.82[JPT][hapmap]
rs2167969	0.80[EUR][1000 genomes]
rs2177698	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs2593442	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs2593474	0.86[CEU][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.85[TSI][hapmap]
rs2602767	0.86[CEU][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap]
rs2602808	0.86[CEU][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.84[TSI][hapmap]
rs2609917	0.86[CEU][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap]
rs2609945	0.87[GIH][hapmap];0.82[JPT][hapmap];0.81[TSI][hapmap]
rs2692035	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4476391	0.81[MKK][hapmap];0.89[YRI][hapmap]
rs4952147	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs6731031	0.86[CEU][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap]
rs6740440	0.86[CEU][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap]
rs6749074	0.81[ASN][1000 genomes]
rs7583211	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs7591110	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs7592355	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs829563	0.85[CEU][hapmap];0.82[JPT][hapmap]
rs829564	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs829565	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs829574	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs829575	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs829578	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs829582	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs829583	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs829618	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs829619	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs829620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs829622	0.93[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs829630	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs829631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs829632	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs829634	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs829641	0.86[ASW][hapmap];0.93[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829642	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829653	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs829654	0.93[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs829659	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs829661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs829662	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs829663	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs829664	0.85[CEU][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap]
rs829669	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829670	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829671	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829672	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829677	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829679	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829681	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs829682	0.92[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs829684	0.86[CEU][hapmap];0.85[JPT][hapmap]
rs829695	0.85[JPT][hapmap]
rs829696	0.85[JPT][hapmap];0.81[TSI][hapmap]
rs829699	0.85[JPT][hapmap]
rs844194	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs860487	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs866680	0.85[CEU][hapmap];0.85[JPT][hapmap]
rs9309680	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533886	chr2:30130019-31068764	ZNF genes & repeats Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs829646	TMEM214	cis	cerebellum	SCAN
rs829646	YPEL5	cis	parietal	SCAN
rs829646	FOSL2	cis	parietal	SCAN
rs829646	EMILIN1	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30697800-30720800	Weak transcription	Thymus	Thymus
2	chr2:30704600-30719600	Weak transcription	Right Atrium	heart
3	chr2:30704600-30719800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr2:30704600-30720600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr2:30711400-30720600	Weak transcription	NHDF-Ad	bronchial
6	chr2:30711600-30723600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr2:30713000-30720600	Weak transcription	Primary T cells from cord blood	blood
8	chr2:30714400-30723600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:30715600-30723800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr2:30715600-30732800	Weak transcription	Hela-S3	cervix
11	chr2:30715800-30721400	Weak transcription	Stomach Mucosa	stomach
12	chr2:30716000-30720400	Weak transcription	Fetal Kidney	kidney
13	chr2:30716000-30720800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr2:30716000-30723800	Weak transcription	Ovary	ovary
15	chr2:30716000-30726000	Weak transcription	Aorta	Aorta
16	chr2:30716000-30727600	Weak transcription	Small Intestine	intestine
17	chr2:30716000-30728000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr2:30716200-30720600	Weak transcription	HSMM	muscle
19	chr2:30716200-30720600	Weak transcription	NHLF	lung
20	chr2:30716200-30726400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:30716200-30726600	Weak transcription	Colon Smooth Muscle	Colon
22	chr2:30716400-30720000	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr2:30716600-30719400	Weak transcription	Fetal Lung	lung
24	chr2:30716600-30720800	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr2:30716600-30723800	Weak transcription	Right Ventricle	heart
26	chr2:30717200-30720600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:30717800-30722600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
28	chr2:30718000-30719600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
29	chr2:30718400-30719400	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr2:30718400-30721600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
31	chr2:30718400-30724600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
32	chr2:30718600-30722000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr2:30719000-30719600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
34	chr2:30719000-30719800	Genic enhancers	Left Ventricle	heart
35	chr2:30719000-30721200	ZNF genes & repeats	Primary B cells from cord blood	blood
36	chr2:30719000-30721400	ZNF genes & repeats	Dnd41	blood
37	chr2:30719200-30719800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr2:30719200-30720000	ZNF genes & repeats	A549	lung

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