Variant report

Variant	rs2726459
Chromosome Location	chr4:106184597-106184598
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:106182085..106183993-chr4:106184382..106185952,2	MCF-7	breast:
2	chr4:106184567..106187118-chr4:106192794..106195271,2	MCF-7	breast:
3	chr4:106176096..106178762-chr4:106183057..106185606,2	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1032625	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10461139	0.89[ASN][1000 genomes]
rs11097882	0.85[ASN][1000 genomes]
rs11721948	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11726786	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11735256	0.87[ASW][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.94[ASN][1000 genomes]
rs12639764	0.86[ASN][1000 genomes]
rs12645144	0.91[ASN][1000 genomes]
rs13103161	0.86[ASN][1000 genomes]
rs13109676	0.91[ASN][1000 genomes]
rs13147502	0.90[ASN][1000 genomes]
rs1391439	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2007403	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[ASN][1000 genomes]
rs2047409	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2133086	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2454205	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2454206	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2466918	0.82[CEU][hapmap]
rs2647244	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2647246	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2647247	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2647248	0.91[EUR][1000 genomes]
rs2647250	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2647251	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2647257	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2647268	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2726460	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2726491	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2726518	0.82[EUR][1000 genomes]
rs2726519	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2726520	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2726521	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34104813	0.90[ASN][1000 genomes]
rs4698932	0.93[GIH][hapmap];0.81[TSI][hapmap]
rs4699165	0.95[ASN][1000 genomes]
rs55838312	0.99[ASN][1000 genomes]
rs62330911	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62331159	0.98[ASN][1000 genomes]
rs62332760	0.98[ASN][1000 genomes]
rs6818637	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6855629	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7658539	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7670522	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7674220	0.80[ASN][1000 genomes]
rs7678440	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes]
rs7683416	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461609	chr4:105869548-106366209	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv470063	chr4:105869548-106366209	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv595007	chr4:105869548-106366209	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv879698	chr4:106155751-106309224	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2726459	TET2	cis	cerebellum	SCAN
rs2726459	OSTC	cis	parietal	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106113600-106195800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr4:106142000-106190800	Weak transcription	Small Intestine	intestine
3	chr4:106148000-106192800	Weak transcription	Psoas Muscle	Psoas
4	chr4:106150200-106191400	Weak transcription	HUVEC	blood vessel
5	chr4:106154000-106198800	Weak transcription	Hela-S3	cervix
6	chr4:106156800-106190800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr4:106156800-106196200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr4:106157000-106186000	Weak transcription	NH-A	brain
9	chr4:106157000-106190400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr4:106157400-106193600	Weak transcription	Colonic Mucosa	Colon
11	chr4:106157800-106190600	Weak transcription	NHLF	lung
12	chr4:106158200-106186600	Weak transcription	Stomach Mucosa	stomach
13	chr4:106158200-106190600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr4:106158200-106190600	Weak transcription	NHEK	skin
15	chr4:106158200-106190800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr4:106158200-106190800	Weak transcription	Pancreas	Pancrea
17	chr4:106158200-106190800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr4:106158200-106190800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr4:106158400-106190000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr4:106158400-106190800	Weak transcription	Gastric	stomach
21	chr4:106158400-106190800	Weak transcription	Lung	lung
22	chr4:106162800-106190800	Weak transcription	Fetal Heart	heart
23	chr4:106163400-106196400	Weak transcription	Brain Angular Gyrus	brain
24	chr4:106163600-106190800	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr4:106165000-106189800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr4:106165200-106190800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr4:106165400-106190000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr4:106165400-106190800	Weak transcription	Stomach Smooth Muscle	stomach
29	chr4:106167400-106193400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr4:106168000-106186200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr4:106168000-106190600	Weak transcription	HSMMtube	muscle
32	chr4:106168000-106190600	Weak transcription	Osteobl	bone
33	chr4:106168000-106190800	Weak transcription	Aorta	Aorta
34	chr4:106168400-106184600	Weak transcription	Rectal Smooth Muscle	rectum
35	chr4:106168400-106186000	Weak transcription	HSMM	muscle
36	chr4:106168600-106193400	Weak transcription	NHDF-Ad	bronchial
37	chr4:106172000-106190800	Weak transcription	Esophagus	oesophagus
38	chr4:106173400-106190600	Weak transcription	Ovary	ovary
39	chr4:106176000-106189800	Weak transcription	Fetal Intestine Small	intestine
40	chr4:106176000-106193200	Weak transcription	Right Ventricle	heart
41	chr4:106176400-106190600	Weak transcription	Fetal Brain Female	brain
42	chr4:106176400-106190800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr4:106176600-106191200	Weak transcription	HMEC	breast
44	chr4:106176800-106190800	Weak transcription	Fetal Brain Male	brain
45	chr4:106178000-106185800	Weak transcription	Brain Anterior Caudate	brain
46	chr4:106178000-106190600	Weak transcription	Brain Hippocampus Middle	brain
47	chr4:106178000-106201000	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr4:106178600-106190400	Weak transcription	Brain Germinal Matrix	brain
49	chr4:106178600-106190800	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr4:106179000-106190600	Weak transcription	Brain Cingulate Gyrus	brain

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