Variant report

Variant	rs7624530
Chromosome Location	chr3:105398093-105398094
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	chr3:105391728..105394638-chr3:105395821..105398573,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114423	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs1042852	1.00[ASW][hapmap];0.81[GIH][hapmap];0.97[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs10446294	0.81[AMR][1000 genomes]
rs10490830	0.92[CHB][hapmap]
rs11706886	0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs11713094	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11915926	0.82[AMR][1000 genomes]
rs11929289	0.83[AMR][1000 genomes]
rs12486371	0.91[ASW][hapmap]
rs12493181	0.83[AMR][1000 genomes]
rs12493560	0.90[CEU][hapmap];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12695122	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12695123	0.83[AMR][1000 genomes]
rs13059405	0.83[AMR][1000 genomes]
rs13061160	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13062734	0.92[CHB][hapmap]
rs13064310	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13065142	0.83[AMR][1000 genomes]
rs13070917	0.85[CHB][hapmap];0.89[ASN][1000 genomes]
rs13073784	0.90[CHB][hapmap]
rs13082334	0.85[CHB][hapmap]
rs13083716	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs13084260	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs13093260	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs13315174	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13317635	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][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];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1443105	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1443106	0.87[AMR][1000 genomes]
rs1443108	0.92[ASW][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes]
rs1530420	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs1545304	0.95[CEU][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17202230	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs17202348	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1867189	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes]
rs1867190	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2083758	0.83[AMR][1000 genomes]
rs2083761	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2120585	0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2244737	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2284993	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2301029	0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2301030	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2301032	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2301037	0.90[CEU][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2301040	0.90[CEU][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2301041	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2301043	0.92[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2301050	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs2301051	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2305035	0.92[ASW][hapmap];0.85[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2305036	0.92[ASW][hapmap];0.90[CEU][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];0.91[MKK][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2305037	0.88[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes]
rs2399054	0.90[CEU][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2399055	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs28532512	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs34520191	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs34896116	0.83[AMR][1000 genomes]
rs35748894	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35834008	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs3732554	0.91[ASN][1000 genomes]
rs3772513	0.86[CHB][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes]
rs3772515	0.92[ASW][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes]
rs3772521	0.93[CHB][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes]
rs3772526	0.86[AMR][1000 genomes]
rs3772527	0.86[AMR][1000 genomes]
rs3772531	0.86[AMR][1000 genomes]
rs3772536	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3772537	0.83[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];0.96[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];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3821488	0.87[CEU][hapmap];0.81[CHB][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4321559	0.83[AMR][1000 genomes]
rs4627779	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6437611	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6437614	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6773661	0.83[AMR][1000 genomes]
rs6796643	0.82[AMR][1000 genomes]
rs726444	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7615317	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7619647	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes]
rs7639888	0.84[ASW][hapmap]
rs7646445	0.87[AMR][1000 genomes]
rs7649520	0.80[AMR][1000 genomes]
rs7652702	0.90[CEU][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs894937	0.86[AMR][1000 genomes]
rs9288815	0.90[CEU][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9657914	0.94[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs9657915	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs9816486	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs9821956	0.81[CEU][hapmap]
rs9840891	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9859953	0.81[CEU][hapmap]
rs9860539	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9870097	0.92[CHB][hapmap];0.84[JPT][hapmap];0.94[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9872897	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9873552	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9876110	0.84[ASW][hapmap]
rs9876767	0.83[AMR][1000 genomes]
rs9877805	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9878058	1.00[CEU][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9880861	0.92[ASW][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes]
rs9883858	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs999046	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525071	chr3:105004853-105409321	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv534224	chr3:105141696-105404293	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv829651	chr3:105203424-105402136	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv877306	chr3:105372196-105495841	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv877307	chr3:105373836-105465189	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv591242	chr3:105373836-105470134	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv877308	chr3:105373836-105495841	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv877309	chr3:105373836-105542435	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv2755185	chr3:105378310-105597310	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7624530	CD47	cis	parietal	SCAN
rs7624530	CBLB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105373000-105419600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:105373400-105401600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:105373600-105419600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr3:105373800-105406200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr3:105375800-105399000	Weak transcription	Dnd41	blood
6	chr3:105375800-105405000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr3:105375800-105419600	Weak transcription	Colonic Mucosa	Colon
8	chr3:105375800-105464600	Weak transcription	Small Intestine	intestine
9	chr3:105376000-105438200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr3:105376800-105440000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr3:105377200-105399200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr3:105378000-105420800	Weak transcription	HUVEC	blood vessel
13	chr3:105378000-105455400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr3:105378600-105438600	Weak transcription	Spleen	Spleen
15	chr3:105379000-105437400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr3:105379200-105440400	Weak transcription	Thymus	Thymus
17	chr3:105380600-105411800	Weak transcription	Brain Substantia Nigra	brain
18	chr3:105382200-105404800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:105382400-105405000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr3:105382800-105404000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr3:105383800-105398600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr3:105384200-105400000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:105384600-105404600	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr3:105385000-105404600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr3:105385200-105404400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr3:105385400-105405200	Strong transcription	Osteobl	bone
27	chr3:105385400-105411000	Weak transcription	HMEC	breast
28	chr3:105385600-105400200	Weak transcription	Fetal Stomach	stomach
29	chr3:105385600-105404400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:105385600-105404400	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr3:105385800-105404400	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr3:105387200-105420800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr3:105388400-105421000	Weak transcription	Gastric	stomach
34	chr3:105388600-105419800	Weak transcription	Brain Germinal Matrix	brain
35	chr3:105388800-105398800	Weak transcription	Brain Hippocampus Middle	brain
36	chr3:105388800-105399000	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr3:105389000-105407200	Weak transcription	HepG2	liver
38	chr3:105389200-105467200	Weak transcription	Stomach Mucosa	stomach
39	chr3:105390800-105403600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:105390800-105404600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr3:105390800-105406800	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr3:105391200-105404600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr3:105391800-105402200	Strong transcription	Fetal Muscle Trunk	muscle
44	chr3:105391800-105402400	Strong transcription	Fetal Lung	lung
45	chr3:105392000-105401600	Strong transcription	Primary B cells from cord blood	blood
46	chr3:105392200-105403200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr3:105392200-105404400	Strong transcription	Placenta	Placenta
48	chr3:105392400-105401200	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr3:105392400-105401800	Strong transcription	NH-A	brain
50	chr3:105392600-105401000	Strong transcription	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links