Variant report

Variant	rs813497
Chromosome Location	chr12:56924116-56924117
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	chr12:56920527..56922162-chr12:56923065..56925052,2	K562	blood:
2	chr12:56916433..56918956-chr12:56923495..56926214,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1043011	0.88[CEU][hapmap]
rs12232026	0.92[JPT][hapmap]
rs2638287	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2638301	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2638315	0.88[CEU][hapmap]
rs2657879	0.88[CEU][hapmap]
rs2657880	0.81[CEU][hapmap]
rs2657896	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2657907	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2694917	0.84[JPT][hapmap];0.88[AMR][1000 genomes]
rs2694919	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2933235	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3759091	0.85[CHB][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs7304944	0.85[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs774211	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs774213	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774215	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs799260	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs799261	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043622	chr12:56571476-56974448	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv541500	chr12:56571476-56974448	Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv899106	chr12:56905558-57004668	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs813497	ORMDL2	cis	parietal	SCAN
rs813497	DCD	cis	parietal	SCAN
rs813497	RBMS2	cis	lymphoblastoid	seeQTL
rs813497	SPRYD4	Cis_1M	lymphoblastoid	RTeQTL
rs813497	LOC283377	cis	multi-tissue	Pritchard
rs813497	SPRYD4	cis	multi-tissue	Pritchard
rs813497	SPRYD4	cis	lymphoblastoid	seeQTL
rs813497	STAC3	cis	parietal	SCAN
rs813497	RBMS2	cis	multi-tissue	Pritchard
rs813497	ITGA5	cis	cerebellum	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56916800-56930400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:56917000-56958000	Weak transcription	Ovary	ovary
3	chr12:56917200-56956200	Weak transcription	Primary T cells from cord blood	blood
4	chr12:56917200-56959200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr12:56917400-56924600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr12:56917400-56931400	Weak transcription	Right Ventricle	heart
7	chr12:56918600-56930000	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr12:56919400-56929600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr12:56919600-56924200	Weak transcription	Spleen	Spleen
10	chr12:56920600-56924800	Enhancers	Placenta	Placenta
11	chr12:56921200-56924400	Weak transcription	HSMMtube	muscle
12	chr12:56921200-56930800	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr12:56921400-56933400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr12:56921400-56956200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr12:56922000-56924600	Weak transcription	Colon Smooth Muscle	Colon
16	chr12:56922000-56924800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr12:56922000-56933000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr12:56922000-56935400	Weak transcription	Fetal Lung	lung
19	chr12:56922200-56928800	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr12:56922400-56925000	Enhancers	Muscle Satellite Cultured Cells	--
21	chr12:56922400-56956200	Weak transcription	HSMM	muscle
22	chr12:56922400-56959200	Weak transcription	Fetal Kidney	kidney
23	chr12:56922800-56924200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr12:56922800-56924400	Weak transcription	Adipose Nuclei	Adipose
25	chr12:56922800-56924600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr12:56922800-56925000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr12:56923000-56924800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr12:56923200-56924200	Weak transcription	Fetal Muscle Leg	muscle
29	chr12:56923200-56924800	Enhancers	NHDF-Ad	bronchial
30	chr12:56923200-56949200	Weak transcription	Fetal Muscle Trunk	muscle
31	chr12:56923400-56924200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr12:56923400-56924600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr12:56923400-56926600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr12:56923400-56926800	Weak transcription	Fetal Stomach	stomach
35	chr12:56923400-56926800	Weak transcription	Left Ventricle	heart
36	chr12:56923400-56929600	Weak transcription	Fetal Intestine Small	intestine
37	chr12:56923400-56931200	Weak transcription	Stomach Smooth Muscle	stomach
38	chr12:56923600-56924200	Weak transcription	Right Atrium	heart
39	chr12:56923600-56924400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr12:56923600-56924400	Weak transcription	NHLF	lung
41	chr12:56923600-56930800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr12:56923600-56931200	Weak transcription	Osteobl	bone
43	chr12:56923600-56933000	Weak transcription	NHEK	skin
44	chr12:56923800-56924200	Weak transcription	A549	lung
45	chr12:56923800-56924200	Weak transcription	HUVEC	blood vessel
46	chr12:56923800-56925200	Enhancers	Hela-S3	cervix
47	chr12:56923800-56926800	Weak transcription	Lung	lung
48	chr12:56923800-56928400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr12:56923800-56930800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr12:56923800-56931000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links