Variant report

Variant	rs7960422
Chromosome Location	chr12:45678032-45678033
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:45668515..45671060-chr12:45676704..45679676,2	K562	blood:
2	chr12:45664849..45667517-chr12:45676358..45678667,2	MCF-7	breast:
3	chr12:45625766..45629467-chr12:45675676..45680562,5	MCF-7	breast:
4	chr12:45609793..45614117-chr12:45674946..45678872,5	MCF-7	breast:
5	chr12:45677746..45679951-chr12:45681323..45682867,2	K562	blood:
6	chr12:45677743..45680287-chr12:45681430..45684437,3	MCF-7	breast:
7	chr12:45608418..45611765-chr12:45675004..45680451,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177119	Chromatin interaction
ENSG00000134297	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1004598	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1019584	0.93[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10748417	0.94[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10748418	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs10748420	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10785559	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10785565	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs10785568	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs10880767	0.90[AMR][1000 genomes]
rs10880773	0.87[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11182971	0.90[AMR][1000 genomes]
rs1238407	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1862907	0.90[AMR][1000 genomes]
rs1877972	0.90[AMR][1000 genomes]
rs1896027	0.88[AFR][1000 genomes]
rs1913691	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2037855	1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4140756	1.00[AMR][1000 genomes]
rs4489808	0.83[AFR][1000 genomes]
rs4768087	0.91[AFR][1000 genomes]
rs4768604	0.90[AMR][1000 genomes]
rs6582542	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6582543	0.90[AMR][1000 genomes]
rs7135029	0.91[AFR][1000 genomes]
rs7953360	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs7970250	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7970619	0.90[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv690	chr12:45674127-45718859	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45654400-45725600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr12:45662800-45685400	Weak transcription	Primary B cells from peripheral blood	blood
3	chr12:45662800-45696800	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr12:45663000-45678200	Weak transcription	Fetal Muscle Trunk	muscle
5	chr12:45663200-45678400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr12:45663400-45680400	Weak transcription	GM12878-XiMat	blood
7	chr12:45664000-45678400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr12:45666200-45709200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr12:45668200-45678200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr12:45668400-45697800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr12:45668600-45679200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr12:45668600-45693000	Weak transcription	Pancreas	Pancrea
13	chr12:45670200-45680600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr12:45674200-45680400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr12:45674200-45706800	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr12:45674400-45679000	Weak transcription	Aorta	Aorta
17	chr12:45674400-45692200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr12:45674600-45678400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr12:45674600-45686400	Weak transcription	K562	blood
20	chr12:45675000-45680600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr12:45675200-45680200	Enhancers	Fetal Intestine Large	intestine
22	chr12:45675400-45679000	Enhancers	Duodenum Mucosa	Duodenum
23	chr12:45675600-45680200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr12:45675800-45678800	Enhancers	Fetal Intestine Small	intestine
25	chr12:45675800-45709000	Weak transcription	Lung	lung
26	chr12:45676000-45679200	Weak transcription	Left Ventricle	heart
27	chr12:45676000-45686600	Weak transcription	Right Atrium	heart
28	chr12:45676200-45693000	Weak transcription	Fetal Stomach	stomach
29	chr12:45676400-45678200	Weak transcription	Gastric	stomach
30	chr12:45676400-45678200	Weak transcription	Ovary	ovary
31	chr12:45676400-45678200	Weak transcription	Thymus	Thymus
32	chr12:45676400-45685600	Weak transcription	Primary B cells from cord blood	blood
33	chr12:45676400-45696000	Weak transcription	Fetal Thymus	thymus
34	chr12:45676400-45697800	Weak transcription	Dnd41	blood
35	chr12:45676400-45740400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr12:45676600-45678600	Enhancers	HUVEC	blood vessel
37	chr12:45676600-45679600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr12:45676800-45678400	Enhancers	Psoas Muscle	Psoas
39	chr12:45676800-45678400	Enhancers	Small Intestine	intestine
40	chr12:45676800-45678600	Enhancers	HepG2	liver
41	chr12:45677000-45678200	Enhancers	Osteobl	bone
42	chr12:45677000-45678800	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr12:45677000-45679000	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr12:45677000-45679200	Enhancers	HMEC	breast
45	chr12:45677000-45679400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr12:45677000-45680000	Enhancers	Placenta Amnion	Placenta Amnion
47	chr12:45677000-45689800	Weak transcription	Liver	Liver
48	chr12:45677000-45696000	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr12:45677200-45678200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr12:45677200-45678600	Enhancers	HSMM	muscle

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