Variant report

Variant	rs10506284
Chromosome Location	chr12:49752651-49752652
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:24)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:24 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49752160..49752717-chr12:49951702..49952277,2	MCF-7	breast:
2	chr12:49721808..49725568-chr12:49752625..49757232,4	MCF-7	breast:
3	chr12:49749944..49753062-chr12:49757524..49761259,4	K562	blood:
4	chr12:49752135..49753715-chr12:49907559..49908688,13	MCF-7	breast:
5	chr12:49752152..49753196-chr12:49947022..49947928,4	K562	blood:
6	chr12:49730335..49732438-chr12:49751228..49753643,2	K562	blood:
7	chr12:49752171..49753157-chr12:49947278..49947948,5	MCF-7	breast:
8	chr12:49752075..49753159-chr12:49973971..49975133,8	MCF-7	breast:
9	chr12:49751555..49753857-chr12:49947807..49949474,2	MCF-7	breast:
10	chr12:49751120..49753975-chr12:49908043..49912245,4	K562	blood:
11	chr12:49751652..49753249-chr12:49945364..49947473,2	MCF-7	breast:
12	chr12:49751231..49754084-chr12:49906021..49909177,3	K562	blood:
13	chr12:49752033..49753621-chr12:49907530..49909179,17	K562	blood:
14	chr12:49749539..49755045-chr12:49758003..49762481,13	MCF-7	breast:
15	chr12:49750309..49752657-chr12:49754226..49756226,3	MCF-7	breast:
16	chr12:49752238..49752947-chr12:49951319..49952178,4	MCF-7	breast:
17	chr12:49751986..49753124-chr12:49905975..49907237,4	K562	blood:
18	chr12:49681831..49682779-chr12:49752157..49753107,3	MCF-7	breast:
19	chr12:49748406..49750091-chr12:49752162..49753928,2	MCF-7	breast:
20	chr12:49751913..49753205-chr12:49907146..49908568,8	MCF-7	breast:
21	chr12:49752289..49753081-chr12:49906577..49907444,2	MCF-7	breast:
22	chr12:49737855..49743235-chr12:49749199..49753144,5	K562	blood:
23	chr12:49691260..49692031-chr12:49752077..49752849,2	MCF-7	breast:
24	chr12:49752159..49753317-chr12:49946994..49947940,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000178401	Chromatin interaction
ENSG00000186897	Chromatin interaction
ENSG00000123352	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10160947	0.83[ASN][1000 genomes]
rs10161131	0.83[ASN][1000 genomes]
rs10506285	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10875948	1.00[CHB][hapmap]
rs11168967	1.00[CHB][hapmap]
rs11168981	1.00[JPT][hapmap]
rs11168988	1.00[ASN][1000 genomes]
rs11169015	1.00[ASN][1000 genomes]
rs11169016	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11169017	1.00[ASN][1000 genomes]
rs11169027	1.00[ASN][1000 genomes]
rs11169048	1.00[CHB][hapmap]
rs11169058	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11169059	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11611743	1.00[ASN][1000 genomes]
rs11831313	1.00[EUR][1000 genomes]
rs11834161	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11835037	1.00[CHB][hapmap]
rs11835071	0.92[EUR][1000 genomes]
rs11837234	1.00[CHB][hapmap]
rs12296440	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12299282	1.00[ASN][1000 genomes]
rs12301632	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12302036	0.83[ASN][1000 genomes]
rs12305716	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12306118	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12306212	1.00[ASN][1000 genomes]
rs12306645	1.00[ASN][1000 genomes]
rs12306866	1.00[JPT][hapmap]
rs12309053	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12310129	1.00[JPT][hapmap]
rs12315996	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12317856	1.00[EUR][1000 genomes]
rs12318618	1.00[CHB][hapmap]
rs12320284	1.00[ASN][1000 genomes]
rs12322319	1.00[ASN][1000 genomes]
rs12322335	1.00[CHB][hapmap]
rs12322561	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12581343	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12581428	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs17123696	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17123751	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs17197593	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1874909	0.96[EUR][1000 genomes]
rs1874910	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes]
rs1874911	0.92[EUR][1000 genomes]
rs2236746	1.00[CHB][hapmap]
rs2270741	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes]
rs2272478	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs28450055	1.00[ASN][1000 genomes]
rs3847764	1.00[CHB][hapmap]
rs57108124	1.00[ASN][1000 genomes]
rs57601151	1.00[ASN][1000 genomes]
rs59250459	1.00[ASN][1000 genomes]
rs60331259	1.00[EUR][1000 genomes]
rs60494978	1.00[EUR][1000 genomes]
rs61340540	1.00[ASN][1000 genomes]
rs6580707	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6580709	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6580710	1.00[ASN][1000 genomes]
rs6580711	1.00[ASN][1000 genomes]
rs6580716	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7132684	1.00[ASN][1000 genomes]
rs7139061	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7294648	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7294973	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7295162	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7295247	1.00[CHB][hapmap]
rs7309997	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs73295291	1.00[ASN][1000 genomes]
rs73295300	1.00[ASN][1000 genomes]
rs73297209	1.00[ASN][1000 genomes]
rs73297210	1.00[ASN][1000 genomes]
rs73297243	1.00[ASN][1000 genomes]
rs7342318	1.00[CHB][hapmap]
rs7342365	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7342384	1.00[CHB][hapmap]
rs74089059	0.92[EUR][1000 genomes]
rs74089062	0.96[EUR][1000 genomes]
rs74089066	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7955541	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7961032	0.83[ASN][1000 genomes]
rs7962951	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7969010	1.00[ASN][1000 genomes]
rs7969099	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7976165	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9919740	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv1042122	chr12:49678529-49823168	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
5	nsv1039176	chr12:49678529-49832618	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
6	nsv899068	chr12:49714103-49924637	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	nsv832405	chr12:49720279-49910862	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10506284	WNT1	cis	brain	seeQTL
rs10506284	HBG1	trans	brain	seeQTL
rs10506284	HBG2	trans	brain	seeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49750600-49753000	Enhancers	HSMM	muscle
2	chr12:49750800-49752800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr12:49750800-49753000	Enhancers	NHDF-Ad	bronchial
4	chr12:49750800-49753800	Enhancers	A549	lung
5	chr12:49751200-49753000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr12:49751200-49753400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr12:49751400-49752800	Enhancers	HSMMtube	muscle
8	chr12:49751400-49753000	Enhancers	NHLF	lung
9	chr12:49751400-49753400	Enhancers	HMEC	breast
10	chr12:49751400-49753800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr12:49751400-49753800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr12:49751400-49753800	Enhancers	NHEK	skin
13	chr12:49752200-49752800	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr12:49752200-49752800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr12:49752200-49753000	Enhancers	Fetal Intestine Large	intestine
16	chr12:49752200-49753000	Enhancers	Fetal Thymus	thymus
17	chr12:49752200-49753000	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr12:49752200-49753200	Enhancers	Hela-S3	cervix
19	chr12:49752200-49754000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr12:49752400-49752800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr12:49752400-49752800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr12:49752400-49752800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr12:49752400-49752800	Enhancers	Liver	Liver
24	chr12:49752400-49752800	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr12:49752400-49752800	Enhancers	NH-A	brain
26	chr12:49752400-49752800	Flanking Active TSS	Osteobl	bone
27	chr12:49752400-49753000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr12:49752400-49753000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
29	chr12:49752400-49753000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr12:49752400-49753000	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr12:49752400-49753000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr12:49752400-49753000	Enhancers	Brain Anterior Caudate	brain
33	chr12:49752400-49753000	Enhancers	Brain Hippocampus Middle	brain
34	chr12:49752400-49753000	Enhancers	Duodenum Mucosa	Duodenum
35	chr12:49752400-49753000	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr12:49752400-49753000	Enhancers	Fetal Intestine Small	intestine
37	chr12:49752400-49753000	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr12:49752400-49753000	Enhancers	Thymus	Thymus
39	chr12:49752400-49753000	Enhancers	Dnd41	blood
40	chr12:49752400-49753000	Enhancers	HUVEC	blood vessel
41	chr12:49752400-49753000	Enhancers	K562	blood
42	chr12:49752400-49753200	Enhancers	Fetal Kidney	kidney
43	chr12:49752400-49753400	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr12:49752600-49752800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr12:49752600-49752800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr12:49752600-49752800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
47	chr12:49752600-49752800	Enhancers	Brain Inferior Temporal Lobe	brain
48	chr12:49752600-49752800	Enhancers	Colon Smooth Muscle	Colon
49	chr12:49752600-49752800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr12:49752600-49753000	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood

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