Variant report

Variant	rs12477340
Chromosome Location	chr2:179728644-179728645
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10497527	0.91[CHD][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes]
rs12464157	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12464703	1.00[AFR][1000 genomes]
rs12468141	0.85[CHB][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12469672	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12476203	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12476289	1.00[AFR][1000 genomes]
rs13400020	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1387472	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1489481	0.85[CHB][hapmap]
rs16866497	1.00[AFR][1000 genomes]
rs16866532	1.00[AFR][1000 genomes]
rs17453396	0.85[CEU][hapmap];0.85[CHB][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17453403	0.85[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1883085	1.00[AFR][1000 genomes]
rs2253324	1.00[AFR][1000 genomes]
rs2291304	1.00[AFR][1000 genomes]
rs2291305	1.00[AFR][1000 genomes]
rs2291308	1.00[AFR][1000 genomes]
rs2306636	1.00[AFR][1000 genomes]
rs2562829	1.00[AFR][1000 genomes]
rs2742357	1.00[AFR][1000 genomes]
rs3769860	1.00[AFR][1000 genomes]
rs4894054	0.85[CHB][hapmap]
rs55800269	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55863869	1.00[AFR][1000 genomes]
rs55913885	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs56030306	1.00[AFR][1000 genomes]
rs56120016	1.00[AFR][1000 genomes]
rs56142888	1.00[AFR][1000 genomes]
rs66677602	1.00[AFR][1000 genomes]
rs72647839	1.00[AFR][1000 genomes]
rs72647889	1.00[AFR][1000 genomes]
rs72648917	1.00[AFR][1000 genomes]
rs966449	0.85[CHB][hapmap]
rs966783	0.85[CEU][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[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	nsv834470	chr2:179555152-179728726	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv934108	chr2:179556852-179729925	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv949133	chr2:179711376-180124327	Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179695800-179738400	Weak transcription	Fetal Intestine Large	intestine
2	chr2:179696400-179728800	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr2:179702200-179749200	Weak transcription	Thymus	Thymus
4	chr2:179702400-179729200	Weak transcription	Lung	lung
5	chr2:179702400-179730000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr2:179710800-179782800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr2:179713400-179729200	Weak transcription	Primary B cells from peripheral blood	blood
8	chr2:179713400-179778600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr2:179717000-179790600	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr2:179718200-179728800	Weak transcription	Primary B cells from cord blood	blood
11	chr2:179722400-179728800	Weak transcription	Aorta	Aorta
12	chr2:179724200-179729600	Weak transcription	Brain Substantia Nigra	brain
13	chr2:179724200-179730400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr2:179724600-179733400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr2:179724800-179729000	Weak transcription	Brain Anterior Caudate	brain
16	chr2:179724800-179730000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:179724800-179732800	Weak transcription	Brain Angular Gyrus	brain
18	chr2:179725800-179729200	Weak transcription	Brain Hippocampus Middle	brain
19	chr2:179726200-179730400	Weak transcription	Fetal Brain Male	brain
20	chr2:179726400-179733400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr2:179726800-179728800	Weak transcription	Left Ventricle	heart
22	chr2:179726800-179729800	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr2:179727000-179729600	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr2:179727800-179728800	Active TSS	Psoas Muscle	Psoas
25	chr2:179727800-179728800	Enhancers	GM12878-XiMat	blood
26	chr2:179727800-179729000	Enhancers	HSMM	muscle
27	chr2:179727800-179729400	Enhancers	Fetal Lung	lung
28	chr2:179727800-179730600	Enhancers	HUVEC	blood vessel
29	chr2:179727800-179730800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr2:179727800-179730800	Enhancers	NHDF-Ad	bronchial
31	chr2:179727800-179731200	Strong transcription	Primary T cells from cord blood	blood
32	chr2:179728000-179728800	Enhancers	Adipose Nuclei	Adipose
33	chr2:179728000-179729000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:179728000-179729600	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr2:179728000-179729800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
36	chr2:179728000-179730400	Enhancers	Brain Germinal Matrix	brain
37	chr2:179728000-179730600	Enhancers	NH-A	brain
38	chr2:179728200-179728800	Enhancers	Fetal Heart	heart
39	chr2:179728200-179729200	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr2:179728200-179729400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr2:179728200-179729400	Flanking Active TSS	NHLF	lung
42	chr2:179728200-179729800	Enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr2:179728200-179753800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr2:179728400-179728800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr2:179728400-179728800	Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr2:179728400-179729000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr2:179728400-179729200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr2:179728400-179729200	Enhancers	NHEK	skin
49	chr2:179728400-179729400	Enhancers	H1 Cell Line	embryonic stem cell
50	chr2:179728400-179729400	Flanking Active TSS	Fetal Muscle Leg	muscle

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