Variant report

Variant	rs2669163
Chromosome Location	chr12:122122566-122122567
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:122122153..122127459-chr12:122235506..122240049,10	MCF-7	breast:
2	chr12:122120133..122122587-chr12:122231814..122234462,2	K562	blood:
3	chr12:122103388..122106454-chr12:122121633..122126620,5	K562	blood:
4	chr12:121903995..121905837-chr12:122120190..122123061,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139725	Chromatin interaction
ENSG00000212694	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10743188	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10840652	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11043179	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12320939	0.96[CEU][hapmap];0.87[CHB][hapmap];0.88[YRI][hapmap];0.87[EUR][1000 genomes]
rs1877484	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2309142	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2669165	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2669166	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2669168	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2720021	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2720022	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2720024	0.83[AMR][1000 genomes]
rs2720025	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2720035	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2942368	0.96[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2942370	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2942379	0.89[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2954116	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3825175	0.92[CEU][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3934658	0.81[CEU][hapmap]
rs6486789	0.87[EUR][1000 genomes]
rs7135617	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs7297028	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7397295	0.83[AFR][1000 genomes]
rs7399127	0.81[CEU][hapmap]
rs7978609	0.86[EUR][1000 genomes]
rs7978866	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053272	chr12:121956483-122132477	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
2	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
3	nsv1040169	chr12:122096825-122209555	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122111400-122124200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr12:122111400-122124400	Weak transcription	Brain Anterior Caudate	brain
3	chr12:122111400-122124800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr12:122111600-122124600	Weak transcription	Fetal Kidney	kidney
5	chr12:122117000-122125800	Weak transcription	K562	blood
6	chr12:122117200-122123800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr12:122117200-122125000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr12:122117400-122123600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr12:122117600-122124200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr12:122117600-122124800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr12:122117800-122124200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr12:122117800-122124800	Weak transcription	Brain Substantia Nigra	brain
13	chr12:122118000-122124200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr12:122118000-122125000	Weak transcription	Brain Germinal Matrix	brain
15	chr12:122118600-122124200	Weak transcription	Placenta	Placenta
16	chr12:122118800-122124400	Weak transcription	Brain Hippocampus Middle	brain
17	chr12:122120000-122124200	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr12:122120200-122124200	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr12:122120200-122124200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr12:122120200-122124400	Weak transcription	Hela-S3	cervix
21	chr12:122120200-122125000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr12:122120400-122123600	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr12:122120400-122123600	Weak transcription	Fetal Thymus	thymus
24	chr12:122120400-122123800	Weak transcription	Primary B cells from peripheral blood	blood
25	chr12:122120400-122123800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr12:122120400-122124200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr12:122120600-122122800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr12:122120600-122123600	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr12:122120600-122123800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr12:122120600-122123800	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr12:122120600-122124200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr12:122121000-122124200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr12:122121800-122149600	Weak transcription	Right Atrium	heart
34	chr12:122122200-122122600	Enhancers	HepG2	liver

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