Variant report

Variant	rs824734
Chromosome Location	chr12:42532139-42532140
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:42532023..42533802-chr12:42623536..42625064,2	K562	blood:
2	chr12:42531740..42536122-chr12:42718714..42721599,4	MCF-7	breast:
3	chr12:42531594..42533278-chr12:42535914..42538108,2	K562	blood:

Variant related genes	Relation type
ENSG00000134283	Chromatin interaction
ENSG00000139168	Chromatin interaction
ENSG00000269367	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1064469	0.83[MEX][hapmap]
rs1069644	0.93[JPT][hapmap]
rs10880275	0.88[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap]
rs10880279	0.88[CHD][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap]
rs1226303	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1238290	0.88[CHD][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap]
rs1463613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1628871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1683195	0.87[MEX][hapmap]
rs1683198	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1683202	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1688854	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1688879	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1688884	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1732351	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];0.83[TSI][hapmap]
rs1732352	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs3852592	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3990966	0.88[MEX][hapmap]
rs6582378	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.92[TSI][hapmap]
rs6582383	0.88[MEX][hapmap]
rs6582392	0.88[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap]
rs712106	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs712119	0.88[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap]
rs712120	0.95[CEU][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs712122	0.93[JPT][hapmap]
rs712123	0.88[CHD][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap]
rs712125	0.93[JPT][hapmap]
rs712129	0.93[JPT][hapmap]
rs7135851	0.88[MEX][hapmap]
rs7297464	0.88[MEX][hapmap]
rs7303028	1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7956016	0.88[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap]
rs7959852	0.88[MEX][hapmap]
rs7960176	0.88[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap]
rs7964383	0.88[MEX][hapmap]
rs7970115	0.87[JPT][hapmap]
rs7971943	0.88[MEX][hapmap]
rs7975518	0.87[MEX][hapmap]
rs7978993	0.93[JPT][hapmap]
rs824697	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs824716	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs824722	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs824724	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs824726	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs824736	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs824738	0.95[CEU][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs824741	0.93[JPT][hapmap]
rs844046	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs865420	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[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	nsv430505	chr12:42297931-42720773	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42493000-42534400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr12:42505800-42537000	Weak transcription	Fetal Stomach	stomach
3	chr12:42505800-42537000	Weak transcription	Lung	lung
4	chr12:42512000-42537400	Weak transcription	Ovary	ovary
5	chr12:42512400-42537000	Weak transcription	Placenta	Placenta
6	chr12:42513000-42537000	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr12:42513200-42537200	Weak transcription	Primary T cells from cord blood	blood
8	chr12:42519000-42537000	Weak transcription	Right Atrium	heart
9	chr12:42519200-42537400	Weak transcription	Small Intestine	intestine
10	chr12:42519600-42537200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:42519800-42536800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr12:42519800-42537000	Weak transcription	Primary B cells from cord blood	blood
13	chr12:42522600-42537000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr12:42524000-42537200	Weak transcription	Aorta	Aorta
15	chr12:42524600-42537000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr12:42524800-42534000	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr12:42524800-42537000	Weak transcription	Fetal Kidney	kidney
18	chr12:42524800-42537000	Weak transcription	Gastric	stomach
19	chr12:42524800-42537200	Weak transcription	Left Ventricle	heart
20	chr12:42524800-42537200	Weak transcription	Psoas Muscle	Psoas
21	chr12:42525400-42535800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr12:42525600-42534800	Weak transcription	HSMM	muscle
23	chr12:42525600-42536800	Weak transcription	HUVEC	blood vessel
24	chr12:42529000-42534400	Weak transcription	Duodenum Mucosa	Duodenum
25	chr12:42529000-42537000	Weak transcription	Fetal Intestine Small	intestine
26	chr12:42529200-42534400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr12:42529200-42534400	Weak transcription	NH-A	brain
28	chr12:42529600-42532800	Weak transcription	GM12878-XiMat	blood
29	chr12:42529600-42534400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr12:42529600-42534600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr12:42529600-42534600	Weak transcription	Osteobl	bone
32	chr12:42529600-42535600	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr12:42529600-42537000	Weak transcription	NHLF	lung
34	chr12:42529800-42534600	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr12:42529800-42534600	Weak transcription	NHDF-Ad	bronchial
36	chr12:42529800-42536600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr12:42529800-42537000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr12:42530000-42534600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr12:42530000-42535800	Weak transcription	Hela-S3	cervix
40	chr12:42530200-42533200	Weak transcription	A549	lung
41	chr12:42530200-42534600	Weak transcription	NHEK	skin
42	chr12:42530400-42534400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr12:42530400-42534400	Weak transcription	HMEC	breast
44	chr12:42530400-42534600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr12:42530600-42534400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr12:42531000-42534800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr12:42531600-42537200	Weak transcription	Right Ventricle	heart
48	chr12:42531800-42537200	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr12:42532000-42532200	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr12:42532000-42534600	Weak transcription	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links