Variant report

Variant	rs2696001
Chromosome Location	chr12:105042417-105042418
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1704885	1.00[ASN][1000 genomes]
rs1704893	1.00[ASN][1000 genomes]
rs1863879	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2559638	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2559644	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2694409	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2694410	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2694411	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2694412	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2694413	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2694415	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2694416	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2695997	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2695998	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2695999	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2696000	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2696002	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs703658	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs727862	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs861346	0.81[EUR][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	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1050695	chr12:105000981-105125161	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv541589	chr12:105000981-105125161	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 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	chr12:105022400-105048200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:105022800-105043200	Weak transcription	Brain Hippocampus Middle	brain
3	chr12:105024600-105044200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr12:105033000-105050200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr12:105033400-105050200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr12:105033600-105050200	Weak transcription	Right Atrium	heart
7	chr12:105035000-105045200	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr12:105035400-105050200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr12:105035800-105054000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr12:105036600-105045200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr12:105037600-105050200	Weak transcription	Osteobl	bone
12	chr12:105038000-105062000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr12:105038400-105042600	Weak transcription	Adipose Nuclei	Adipose
14	chr12:105038400-105044000	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr12:105038400-105050400	Weak transcription	Stomach Smooth Muscle	stomach
16	chr12:105038400-105051600	Weak transcription	Aorta	Aorta
17	chr12:105038400-105053000	Weak transcription	NHEK	skin
18	chr12:105038400-105055400	Weak transcription	Gastric	stomach
19	chr12:105038400-105061200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr12:105038400-105062600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr12:105038600-105043200	Weak transcription	Brain Anterior Caudate	brain
22	chr12:105038600-105043200	Weak transcription	Small Intestine	intestine
23	chr12:105038600-105043400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr12:105038600-105043600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr12:105038600-105043600	Weak transcription	Brain Germinal Matrix	brain
26	chr12:105038600-105043600	Weak transcription	Duodenum Mucosa	Duodenum
27	chr12:105038600-105044400	Weak transcription	Left Ventricle	heart
28	chr12:105038600-105045000	Weak transcription	Placenta	Placenta
29	chr12:105038600-105045600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr12:105038600-105046600	Weak transcription	Pancreas	Pancrea
31	chr12:105038600-105047200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr12:105038600-105050400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr12:105038600-105057600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr12:105038600-105061000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr12:105038600-105061400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr12:105038600-105062400	Weak transcription	HMEC	breast
37	chr12:105038600-105062800	Weak transcription	Esophagus	oesophagus
38	chr12:105038600-105063200	Weak transcription	Primary T cells from cord blood	blood
39	chr12:105038800-105045600	Weak transcription	Brain Substantia Nigra	brain
40	chr12:105038800-105047200	Weak transcription	K562	blood
41	chr12:105038800-105051000	Weak transcription	GM12878-XiMat	blood
42	chr12:105039200-105062200	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr12:105039400-105042600	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr12:105039400-105045200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr12:105039800-105043200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr12:105040000-105043600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr12:105040200-105042600	Weak transcription	Lung	lung
48	chr12:105040400-105043600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr12:105040800-105046800	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr12:105041000-105042600	Weak transcription	Brain Angular Gyrus	brain

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