Variant report

Variant	rs829575
Chromosome Location	chr2:30680633-30680634
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:30668373..30671369-chr2:30677900..30680714,3	MCF-7	breast:
2	chr2:30676770..30678569-chr2:30680494..30682034,2	K562	blood:
3	chr2:30677517..30682510-chr2:30682594..30687236,9	K562	blood:
4	chr2:30678530..30680872-chr2:30685623..30687236,2	K562	blood:

Variant related genes	Relation type
ENSG00000172954	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10167083	0.93[CEU][hapmap];0.85[JPT][hapmap]
rs10175399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10183928	0.92[CEU][hapmap];0.85[JPT][hapmap]
rs12053428	0.93[CEU][hapmap];0.85[JPT][hapmap]
rs12468064	0.93[CEU][hapmap];0.85[JPT][hapmap]
rs1252624	0.89[EUR][1000 genomes]
rs1252625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs1252631	0.93[CEU][hapmap];0.85[JPT][hapmap]
rs1252646	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs1252651	0.93[CEU][hapmap];0.85[JPT][hapmap]
rs1252654	1.00[JPT][hapmap]
rs1525062	0.93[CEU][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap]
rs17009706	0.82[YRI][hapmap]
rs1869423	0.93[CEU][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap]
rs1869424	0.93[CEU][hapmap];0.94[GIH][hapmap];0.84[TSI][hapmap]
rs1975555	0.93[CEU][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap]
rs2121600	0.93[CEU][hapmap]
rs2123753	0.93[CEU][hapmap];0.82[JPT][hapmap]
rs2167969	0.87[EUR][1000 genomes]
rs2177698	0.93[CEU][hapmap];0.85[JPT][hapmap]
rs2593442	0.93[CEU][hapmap];0.85[JPT][hapmap]
rs2593474	0.93[CEU][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.89[TSI][hapmap]
rs2602767	0.93[CEU][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap]
rs2602808	0.93[CEU][hapmap];0.92[GIH][hapmap];0.85[JPT][hapmap];0.88[TSI][hapmap]
rs2609917	0.93[CEU][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap]
rs2609945	0.86[CEU][hapmap];0.86[GIH][hapmap];0.82[JPT][hapmap];0.85[TSI][hapmap]
rs2692035	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4476391	0.86[YRI][hapmap]
rs4952147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes]
rs6731031	0.93[CEU][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap]
rs6740440	0.93[CEU][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap]
rs6749074	0.86[EUR][1000 genomes]
rs7583211	0.93[CEU][hapmap];0.85[JPT][hapmap]
rs7591110	0.93[CEU][hapmap];0.85[JPT][hapmap]
rs7592355	0.93[CEU][hapmap];0.85[JPT][hapmap]
rs829563	0.92[CEU][hapmap];0.82[JPT][hapmap]
rs829564	0.93[CEU][hapmap];0.85[JPT][hapmap]
rs829565	0.93[CEU][hapmap];0.85[JPT][hapmap]
rs829574	0.93[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829578	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829582	0.93[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs829583	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs829618	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.89[EUR][1000 genomes]
rs829619	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs829620	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs829622	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs829630	0.93[CEU][hapmap];0.85[JPT][hapmap]
rs829631	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs829632	0.93[CEU][hapmap];0.85[JPT][hapmap]
rs829634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs829641	0.86[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829642	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829646	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]
rs829653	0.93[CEU][hapmap];0.85[JPT][hapmap]
rs829654	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829655	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs829659	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs829661	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs829662	0.85[EUR][1000 genomes]
rs829663	0.85[EUR][1000 genomes]
rs829664	0.92[CEU][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.89[TSI][hapmap]
rs829669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829670	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829671	0.93[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829672	0.93[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829673	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs829675	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829677	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829680	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs829681	0.93[CEU][hapmap];0.85[JPT][hapmap]
rs829682	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs829684	0.93[CEU][hapmap];0.85[JPT][hapmap]
rs829695	0.85[JPT][hapmap]
rs829696	0.85[JPT][hapmap];0.85[TSI][hapmap]
rs829699	0.85[JPT][hapmap]
rs844194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs860487	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs866680	0.92[CEU][hapmap];0.85[JPT][hapmap]
rs9309680	0.82[EUR][1000 genomes]

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	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
2	nsv833648	chr2:30505882-30696275	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs829575	FOSL2	cis	parietal	SCAN
rs829575	TMEM214	cis	cerebellum	SCAN
rs829575	YPEL5	cis	parietal	SCAN
rs829575	LYCAT	cis	multi-tissue	Pritchard
rs829575	EMILIN1	cis	parietal	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30671000-30682000	Weak transcription	Aorta	Aorta
2	chr2:30671000-30685200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:30671200-30681200	Weak transcription	Right Atrium	heart
4	chr2:30671200-30688200	Weak transcription	HSMM	muscle
5	chr2:30671600-30682000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:30671600-30682000	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr2:30671600-30683800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr2:30671600-30685600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr2:30671600-30688000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr2:30671600-30688200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:30671600-30694600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr2:30671600-30703400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr2:30671600-30704200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:30671800-30681400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr2:30672000-30681000	Weak transcription	Primary B cells from peripheral blood	blood
16	chr2:30672000-30681200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr2:30672000-30681800	Weak transcription	Primary B cells from cord blood	blood
18	chr2:30672000-30682000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr2:30672000-30684600	Weak transcription	Hela-S3	cervix
20	chr2:30672000-30686400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr2:30672000-30686800	Weak transcription	Dnd41	blood
22	chr2:30672000-30688000	Weak transcription	Fetal Lung	lung
23	chr2:30672800-30682600	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr2:30673600-30681400	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr2:30673800-30681400	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr2:30674200-30687400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:30675800-30681600	Weak transcription	Primary T cells from cord blood	blood
28	chr2:30675800-30682000	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr2:30675800-30682200	Enhancers	HepG2	liver
30	chr2:30676200-30681200	Weak transcription	Psoas Muscle	Psoas
31	chr2:30677400-30681800	Enhancers	Fetal Intestine Large	intestine
32	chr2:30677800-30683800	Enhancers	Fetal Heart	heart
33	chr2:30678200-30684200	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr2:30678200-30684200	Weak transcription	A549	lung
35	chr2:30678400-30682000	Weak transcription	Right Ventricle	heart
36	chr2:30678400-30682400	Weak transcription	Gastric	stomach
37	chr2:30678400-30704200	Weak transcription	Fetal Stomach	stomach
38	chr2:30678600-30681800	Weak transcription	Stomach Mucosa	stomach
39	chr2:30678600-30688000	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr2:30678600-30703800	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr2:30678600-30710600	Weak transcription	NHLF	lung
42	chr2:30678800-30681000	Weak transcription	Small Intestine	intestine
43	chr2:30678800-30687800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr2:30679000-30682600	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr2:30679000-30683600	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr2:30679000-30684200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr2:30679200-30688000	Weak transcription	Pancreas	Pancrea
48	chr2:30679400-30681200	Weak transcription	Ovary	ovary
49	chr2:30679400-30681200	Weak transcription	GM12878-XiMat	blood
50	chr2:30679400-30682000	Weak transcription	H9 Cell Line	embryonic stem cell

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