Variant report

Variant	rs235617
Chromosome Location	chr12:47052746-47052747
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:46831691..46833742-chr12:47051403..47054145,2	K562	blood:
2	chr12:46759450..46767729-chr12:47050364..47062392,28	MCF-7	breast:
3	chr12:46885416..46887111-chr12:47052344..47054021,2	MCF-7	breast:
4	chr12:46760654..46769647-chr12:47051646..47061944,32	MCF-7	breast:
5	chr12:46762091..46764128-chr12:47051293..47053503,2	K562	blood:
6	chr12:46762091..46766718-chr12:47051293..47055848,8	K562	blood:
7	chr12:46745913..46748762-chr12:47052132..47055018,2	K562	blood:

Variant related genes	Relation type
ENSG00000134294	Chromatin interaction
ENSG00000258096	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10785631	1.00[CEU][hapmap]
rs10880975	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs10880976	1.00[CEU][hapmap]
rs10880977	1.00[CEU][hapmap]
rs11183497	1.00[CEU][hapmap]
rs11183539	0.88[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11183547	0.88[AMR][1000 genomes]
rs11183550	0.90[AMR][1000 genomes]
rs11829502	1.00[CEU][hapmap]
rs11831177	1.00[CEU][hapmap]
rs11831920	1.00[CEU][hapmap]
rs11831929	1.00[CEU][hapmap]
rs11836915	1.00[CEU][hapmap]
rs11836940	1.00[CEU][hapmap]
rs12300125	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap]
rs12310635	0.83[AMR][1000 genomes]
rs12320420	0.82[AMR][1000 genomes]
rs12580121	1.00[CEU][hapmap]
rs12581311	0.87[AMR][1000 genomes]
rs12582056	1.00[CEU][hapmap];0.88[AMR][1000 genomes]
rs12582305	1.00[CEU][hapmap]
rs17096991	1.00[CEU][hapmap]
rs17096995	1.00[CEU][hapmap]
rs17097002	1.00[CEU][hapmap]
rs17097022	1.00[CEU][hapmap]
rs17121410	1.00[CEU][hapmap]
rs17121412	1.00[CEU][hapmap]
rs2042058	1.00[CEU][hapmap];0.85[AMR][1000 genomes]
rs235600	0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs235601	0.94[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs235602	0.94[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs235607	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs235610	0.94[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs235616	0.96[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs235621	1.00[CEU][hapmap];0.90[AMR][1000 genomes]
rs235622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs235625	0.96[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs235626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.96[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs235627	0.90[AMR][1000 genomes]
rs2430940	1.00[CEU][hapmap];0.81[JPT][hapmap]
rs2430942	1.00[CEU][hapmap]
rs2430946	1.00[CEU][hapmap]
rs2430947	1.00[CEU][hapmap]
rs2471583	1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2471594	1.00[CEU][hapmap]
rs2471602	1.00[CEU][hapmap]
rs2471605	1.00[CEU][hapmap]
rs2471608	1.00[CEU][hapmap]
rs2471618	1.00[CEU][hapmap]
rs2909411	1.00[CEU][hapmap]
rs34008890	0.88[AMR][1000 genomes]
rs35096979	0.88[AMR][1000 genomes]
rs4768741	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4768742	0.88[AMR][1000 genomes]
rs4768744	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs57370043	0.87[AMR][1000 genomes]
rs58561072	0.85[AMR][1000 genomes]
rs61641663	0.85[AMR][1000 genomes]
rs6582666	1.00[CEU][hapmap]
rs7295471	1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap]
rs7310326	1.00[CEU][hapmap]
rs7310408	0.88[AMR][1000 genomes]
rs73282109	0.90[AMR][1000 genomes]
rs7484802	0.90[AMR][1000 genomes]
rs977069	1.00[CEU][hapmap];0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
3	esv3416674	chr12:46988689-47178369	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv558783	chr12:46996632-47144856	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv1844378	chr12:47028797-47072016	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	esv1845143	chr12:47051076-47431496	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47041000-47054200	Weak transcription	Fetal Kidney	kidney
2	chr12:47042200-47054800	Weak transcription	Fetal Intestine Small	intestine
3	chr12:47043400-47053800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr12:47046400-47069800	Weak transcription	Pancreas	Pancrea
5	chr12:47046800-47057000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:47048600-47053000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr12:47049200-47053600	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr12:47049400-47053400	Weak transcription	Primary B cells from cord blood	blood
9	chr12:47050600-47052800	Weak transcription	Aorta	Aorta
10	chr12:47050800-47052800	Enhancers	Osteobl	bone
11	chr12:47050800-47053000	Enhancers	Adipose Nuclei	Adipose
12	chr12:47050800-47053000	Weak transcription	HepG2	liver
13	chr12:47050800-47053000	Enhancers	NHDF-Ad	bronchial
14	chr12:47050800-47055000	Enhancers	Muscle Satellite Cultured Cells	--
15	chr12:47050800-47056000	Enhancers	NHLF	lung
16	chr12:47051000-47052800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr12:47051000-47052800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr12:47051000-47053000	Weak transcription	Right Atrium	heart
19	chr12:47051000-47055000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr12:47051000-47056200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr12:47051200-47055000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr12:47051400-47053000	Enhancers	Rectal Smooth Muscle	rectum
23	chr12:47051400-47053000	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr12:47051400-47054600	Enhancers	A549	lung
25	chr12:47051400-47055600	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr12:47051400-47055800	Enhancers	Fetal Heart	heart
27	chr12:47051400-47055800	Enhancers	HSMM	muscle
28	chr12:47051400-47056200	Enhancers	HUVEC	blood vessel
29	chr12:47051400-47059800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr12:47051600-47053000	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr12:47051600-47053000	Enhancers	NHEK	skin
32	chr12:47051600-47053200	Enhancers	Dnd41	blood
33	chr12:47051600-47055600	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr12:47051800-47052800	Enhancers	Colon Smooth Muscle	Colon
35	chr12:47051800-47053400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr12:47051800-47053400	Enhancers	HSMMtube	muscle
37	chr12:47051800-47054200	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr12:47051800-47055000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr12:47051800-47055400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr12:47051800-47056000	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr12:47051800-47056000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr12:47052000-47052800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr12:47052000-47053000	Weak transcription	Psoas Muscle	Psoas
44	chr12:47052000-47053000	Weak transcription	NH-A	brain
45	chr12:47052000-47053600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr12:47052000-47054200	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr12:47052000-47054400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr12:47052200-47052800	Enhancers	Stomach Smooth Muscle	stomach
49	chr12:47052200-47053800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr12:47052200-47053800	Weak transcription	Ovary	ovary

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