Variant report

Variant	rs7138247
Chromosome Location	chr12:45669753-45669754
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:45608183..45610054-chr12:45668123..45670061,2	MCF-7	breast:
2	chr12:45625441..45631111-chr12:45668814..45675582,6	MCF-7	breast:
3	chr12:45668006..45670092-chr12:45670299..45672626,2	MCF-7	breast:
4	chr12:45668515..45671060-chr12:45676704..45679676,2	K562	blood:
5	chr12:45668554..45670419-chr12:45671856..45674022,2	K562	blood:
6	chr12:45608744..45610337-chr12:45668479..45671115,2	K562	blood:

Variant related genes	Relation type
ENSG00000134297	Chromatin interaction
ENSG00000177119	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1015626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1025088	0.91[LWK][hapmap];0.88[MKK][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes]
rs10459295	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs10467095	0.81[YRI][hapmap]
rs10736024	0.82[YRI][hapmap];0.82[AFR][1000 genomes]
rs10748412	0.84[ASN][1000 genomes]
rs10748416	0.81[AFR][1000 genomes]
rs10785564	0.82[YRI][hapmap];0.83[AFR][1000 genomes]
rs10785566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10785569	0.90[TSI][hapmap]
rs10880761	0.86[JPT][hapmap]
rs10880762	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs10880764	0.82[CHB][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.80[MEX][hapmap]
rs10880765	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs10880766	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs10880768	0.87[EUR][1000 genomes]
rs10880771	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11182905	0.80[CHB][hapmap];0.86[JPT][hapmap]
rs11182918	0.86[JPT][hapmap]
rs11182949	0.82[CHB][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap]
rs11182954	0.82[CEU][hapmap]
rs11182955	0.82[CEU][hapmap]
rs11182957	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs11182961	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs11182965	0.82[CEU][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs11182966	0.87[EUR][1000 genomes]
rs11182969	0.87[EUR][1000 genomes]
rs11182970	0.87[EUR][1000 genomes]
rs11182973	0.82[EUR][1000 genomes]
rs11182974	0.82[EUR][1000 genomes]
rs11182980	0.85[ASW][hapmap]
rs11182981	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs11182986	0.90[TSI][hapmap]
rs11182988	0.90[TSI][hapmap]
rs11183014	0.90[TSI][hapmap]
rs11183029	0.90[TSI][hapmap]
rs11614082	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs11614089	0.87[EUR][1000 genomes]
rs12228399	0.87[EUR][1000 genomes]
rs12230322	0.86[JPT][hapmap]
rs12231753	0.86[JPT][hapmap]
rs12297071	0.90[TSI][hapmap]
rs12320168	0.89[GIH][hapmap];0.86[JPT][hapmap]
rs12815577	1.00[CEU][hapmap];0.86[CHB][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs1399721	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1863549	0.90[TSI][hapmap]
rs1913690	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1913692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2012937	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2037856	0.82[YRI][hapmap];0.83[AFR][1000 genomes]
rs2037857	0.82[YRI][hapmap];0.83[AFR][1000 genomes]
rs2052603	0.82[CHB][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap]
rs2408184	0.89[GIH][hapmap];0.86[JPT][hapmap]
rs34759896	0.87[EUR][1000 genomes]
rs35032811	0.87[EUR][1000 genomes]
rs35400022	0.82[EUR][1000 genomes]
rs3803178	0.90[TSI][hapmap]
rs4326862	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4768085	1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.84[ASN][1000 genomes]
rs4768598	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4768600	1.00[YRI][hapmap];0.99[AFR][1000 genomes]
rs4768601	1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4768602	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4768603	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4768605	0.96[AFR][1000 genomes]
rs4768606	0.85[ASW][hapmap]
rs6582541	1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7136281	0.91[LWK][hapmap];0.82[MKK][hapmap];0.81[YRI][hapmap]
rs7136368	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs728590	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7304481	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.84[ASN][1000 genomes]
rs7304749	0.85[ASW][hapmap]
rs7307262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7309615	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7310046	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7487910	0.83[ASN][1000 genomes]
rs7965430	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[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	nsv1050923	chr12:45581310-45808289	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45651400-45675600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr12:45651600-45674000	Weak transcription	Primary B cells from cord blood	blood
3	chr12:45654400-45725600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr12:45662800-45677400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr12:45662800-45685400	Weak transcription	Primary B cells from peripheral blood	blood
6	chr12:45662800-45696800	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr12:45663000-45670000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr12:45663000-45677400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr12:45663000-45677600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:45663000-45678200	Weak transcription	Fetal Muscle Trunk	muscle
11	chr12:45663200-45674000	Weak transcription	Dnd41	blood
12	chr12:45663200-45678400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr12:45663400-45672200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr12:45663400-45677400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr12:45663400-45677400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr12:45663400-45680400	Weak transcription	GM12878-XiMat	blood
17	chr12:45663600-45674400	Weak transcription	Primary hematopoietic stem cells	blood
18	chr12:45663600-45677000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr12:45664000-45672200	Weak transcription	Liver	Liver
20	chr12:45664000-45676000	Weak transcription	Fetal Stomach	stomach
21	chr12:45664000-45678400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr12:45664200-45669800	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr12:45664400-45677600	Weak transcription	Fetal Kidney	kidney
24	chr12:45665000-45673600	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr12:45665600-45676000	Weak transcription	Thymus	Thymus
26	chr12:45666200-45709200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr12:45666600-45670600	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr12:45667000-45670400	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr12:45667200-45670200	Enhancers	Psoas Muscle	Psoas
30	chr12:45667400-45670400	Enhancers	Placenta Amnion	Placenta Amnion
31	chr12:45667600-45670200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr12:45668000-45669800	Weak transcription	Fetal Lung	lung
33	chr12:45668000-45670000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr12:45668000-45670000	Weak transcription	Esophagus	oesophagus
35	chr12:45668000-45670000	Weak transcription	Stomach Smooth Muscle	stomach
36	chr12:45668000-45672600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr12:45668000-45677400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr12:45668200-45672400	Weak transcription	Primary T cells from cord blood	blood
39	chr12:45668200-45676000	Weak transcription	Gastric	stomach
40	chr12:45668200-45677400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr12:45668200-45678200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr12:45668400-45670200	Enhancers	K562	blood
43	chr12:45668400-45670600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr12:45668400-45674200	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr12:45668400-45675400	Weak transcription	Duodenum Mucosa	Duodenum
46	chr12:45668400-45697800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr12:45668600-45669800	Weak transcription	Placenta	Placenta
48	chr12:45668600-45670000	Weak transcription	Small Intestine	intestine
49	chr12:45668600-45670200	Weak transcription	Rectal Smooth Muscle	rectum
50	chr12:45668600-45672600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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