Variant report

Variant	rs2412963
Chromosome Location	chr22:30391281-30391282
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:30231401..30237558-chr22:30387473..30391733,6	MCF-7	breast:
2	chr22:30387371..30390104-chr22:30390840..30392967,2	MCF-7	breast:
3	chr22:30210116..30212715-chr22:30390306..30391990,2	MCF-7	breast:
4	chr22:30388182..30392809-chr22:30393222..30398050,6	K562	blood:
5	chr22:30388710..30391580-chr22:30397983..30401344,3	MCF-7	breast:
6	chr22:30388182..30391432-chr22:30393585..30396816,3	K562	blood:

Variant related genes	Relation type
ENSG00000100330	Chromatin interaction
ENSG00000100325	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1071888	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1076137	0.91[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap]
rs11090598	0.83[EUR][1000 genomes]
rs12168499	0.83[EUR][1000 genomes]
rs12168552	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12171061	0.88[EUR][1000 genomes]
rs12171250	0.81[EUR][1000 genomes]
rs12537	0.80[CEU][hapmap]
rs17643918	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17648725	0.83[EUR][1000 genomes]
rs1807509	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs193473	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs193481	0.90[EUR][1000 genomes]
rs2017677	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2051764	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2105870	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2349225	0.91[CEU][hapmap];0.89[JPT][hapmap]
rs2412960	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28257	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34862234	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35705048	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36578	0.89[JPT][hapmap]
rs36580	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36590	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36591	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36594	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36596	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36598	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36601	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36604	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36605	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs36606	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36607	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3788423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3887275	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3958025	0.91[CEU][hapmap];0.88[CHB][hapmap];0.88[JPT][hapmap]
rs39712	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41162	0.95[CEU][hapmap];0.92[EUR][1000 genomes]
rs41164	0.91[CEU][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs41166	0.86[EUR][1000 genomes]
rs41172	0.83[CEU][hapmap]
rs41174	0.82[CEU][hapmap]
rs41175	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs41179	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4239932	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4239933	0.83[EUR][1000 genomes]
rs4337577	0.83[EUR][1000 genomes]
rs4823063	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4823070	0.82[EUR][1000 genomes]
rs4993442	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs5752968	0.91[CEU][hapmap];0.88[CHB][hapmap];0.86[JPT][hapmap]
rs5752986	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5752988	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5752993	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763630	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5763634	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5763644	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5763674	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5763675	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763680	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5763689	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5763691	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs715523	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs718772	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs7286070	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7292615	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs737904	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs737909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737912	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7510705	0.83[EUR][1000 genomes]
rs8135823	0.83[EUR][1000 genomes]
rs8136147	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8139994	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8141404	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs8141680	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9620926	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9620943	0.86[EUR][1000 genomes]
rs9620953	0.80[EUR][1000 genomes]
rs9625873	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9625874	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9625878	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9625879	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9625919	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs9625926	0.83[EUR][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	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30350600-30402600	Weak transcription	Aorta	Aorta
2	chr22:30363400-30427800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr22:30367000-30426600	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr22:30367400-30397800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr22:30373800-30391400	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr22:30375200-30403200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr22:30376200-30394800	Weak transcription	GM12878-XiMat	blood
8	chr22:30377600-30402800	Weak transcription	Fetal Brain Male	brain
9	chr22:30378200-30398800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr22:30378400-30391400	Strong transcription	Primary B cells from peripheral blood	blood
11	chr22:30380800-30391800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr22:30381000-30397600	Weak transcription	Fetal Kidney	kidney
13	chr22:30382600-30392000	Strong transcription	Primary T cells from cord blood	blood
14	chr22:30383800-30391600	Strong transcription	Primary B cells from cord blood	blood
15	chr22:30384200-30398400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr22:30384200-30403800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr22:30384400-30393400	Weak transcription	Brain Hippocampus Middle	brain
18	chr22:30384400-30404000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr22:30385000-30404000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr22:30386200-30402600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr22:30387600-30391400	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr22:30388000-30394400	Weak transcription	Lung	lung
23	chr22:30388000-30394600	Weak transcription	Fetal Lung	lung
24	chr22:30388000-30398400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr22:30388200-30391800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr22:30388200-30392200	Enhancers	HMEC	breast
27	chr22:30388400-30391800	Enhancers	NH-A	brain
28	chr22:30388400-30392200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr22:30388400-30392200	Enhancers	Muscle Satellite Cultured Cells	--
30	chr22:30388600-30396800	Weak transcription	Brain Germinal Matrix	brain
31	chr22:30388600-30398200	Weak transcription	Spleen	Spleen
32	chr22:30388600-30400800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr22:30388800-30391600	Enhancers	Osteobl	bone
34	chr22:30388800-30391800	Enhancers	HSMM	muscle
35	chr22:30389000-30391600	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr22:30389000-30398600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr22:30389200-30391800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr22:30389200-30392800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr22:30389200-30394800	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr22:30389200-30398400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr22:30389200-30402600	Weak transcription	Rectal Smooth Muscle	rectum
42	chr22:30389200-30403000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr22:30389200-30404200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr22:30389200-30409200	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr22:30389200-30411600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr22:30389200-30411800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr22:30389400-30392000	Enhancers	Pancreatic Islets	Pancreatic Islet
48	chr22:30389400-30393400	Weak transcription	Colon Smooth Muscle	Colon
49	chr22:30389400-30394800	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr22:30389400-30398200	Weak transcription	Thymus	Thymus

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