Variant report

Variant	rs2587021
Chromosome Location	chr3:146254116-146254117
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:146254115..146256698-chr3:146261297..146263941,3	MCF-7	breast:
2	chr3:146245382..146249214-chr3:146253354..146257434,4	K562	blood:
3	chr3:146251866..146257697-chr3:146260468..146262994,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000188313	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1057481	0.91[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1061307	0.84[YRI][hapmap]
rs1079369	0.95[CEU][hapmap];0.82[JPT][hapmap]
rs13064509	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs13069082	0.82[JPT][hapmap]
rs13074501	0.82[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs1373246	0.91[CEU][hapmap];0.82[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1443827	0.82[JPT][hapmap]
rs1546420	0.89[ASN][1000 genomes]
rs1546421	0.89[ASN][1000 genomes]
rs1579786	0.87[ASN][1000 genomes]
rs1579787	0.87[ASN][1000 genomes]
rs16858420	0.83[JPT][hapmap];0.89[YRI][hapmap]
rs1882971	0.97[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1882972	0.95[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1882973	0.95[CEU][hapmap];0.82[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1882974	0.95[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1997601	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs1997604	0.82[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes]
rs2083866	0.87[ASN][1000 genomes]
rs2120381	0.95[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2165948	0.90[CEU][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2587007	0.81[AFR][1000 genomes]
rs2587008	0.87[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2587009	0.84[EUR][1000 genomes]
rs2587010	0.97[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2587011	0.91[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2587012	0.91[CEU][hapmap];0.83[JPT][hapmap];0.84[EUR][1000 genomes]
rs2587013	0.91[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2587014	0.95[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2587015	0.91[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2587016	0.91[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2587017	0.90[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2587018	0.91[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2587023	0.91[CEU][hapmap];0.83[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2587024	0.95[CEU][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2609860	0.95[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2609861	0.95[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2609862	0.84[EUR][1000 genomes]
rs2609864	0.91[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2609865	0.91[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2609866	0.95[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2609867	0.97[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2688688	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs2688693	0.82[JPT][hapmap]
rs2738905	0.91[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2738906	0.95[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2738907	0.95[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2738910	0.91[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2738911	0.91[CEU][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs2738912	0.91[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2738915	0.87[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2738916	0.91[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2738918	0.91[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2738920	0.87[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2738921	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2738923	0.91[CEU][hapmap];0.83[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs34682680	0.82[ASN][1000 genomes]
rs35046242	0.89[ASN][1000 genomes]
rs35416584	0.89[ASN][1000 genomes]
rs3773510	0.97[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs7615988	0.83[JPT][hapmap]
rs7639636	0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs9289722	0.91[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs977757	0.89[ASN][1000 genomes]
rs977759	0.89[ASN][1000 genomes]
rs9810169	0.87[ASN][1000 genomes]
rs9813199	0.82[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs9832220	0.83[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs9833135	0.83[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs9861142	0.82[JPT][hapmap]
rs9876886	0.95[CEU][hapmap];0.82[JPT][hapmap]

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	esv3448053	chr3:146186791-146262066	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv3523751	chr3:146186838-146261806	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	esv3523753	chr3:146186838-146261806	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	esv2496437	chr3:146186902-146262961	Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:146224800-146254400	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr3:146225400-146255000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr3:146225400-146256600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:146225400-146257000	Weak transcription	Right Ventricle	heart
5	chr3:146225400-146260800	Weak transcription	NH-A	brain
6	chr3:146225600-146258600	Weak transcription	Brain Hippocampus Middle	brain
7	chr3:146229000-146259600	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr3:146229800-146257000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:146231600-146254400	Weak transcription	Brain Anterior Caudate	brain
10	chr3:146231600-146254400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr3:146231600-146257200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr3:146231600-146258600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr3:146231600-146259000	Weak transcription	Brain Angular Gyrus	brain
14	chr3:146231600-146260800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr3:146231800-146254400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:146232000-146257400	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr3:146232000-146259600	Weak transcription	NHDF-Ad	bronchial
18	chr3:146232800-146254400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr3:146232800-146256000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:146233000-146255200	Weak transcription	Esophagus	oesophagus
21	chr3:146233000-146259800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr3:146233000-146261400	Weak transcription	Fetal Muscle Trunk	muscle
23	chr3:146233600-146259200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr3:146234400-146258000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr3:146236200-146254400	Weak transcription	Gastric	stomach
26	chr3:146236200-146254600	Weak transcription	Spleen	Spleen
27	chr3:146237000-146254400	Weak transcription	Brain Substantia Nigra	brain
28	chr3:146237400-146254400	Weak transcription	Stomach Mucosa	stomach
29	chr3:146240000-146254600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr3:146240400-146257200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr3:146240800-146254400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr3:146241400-146254400	Weak transcription	Small Intestine	intestine
33	chr3:146241800-146255000	Weak transcription	Lung	lung
34	chr3:146241800-146258600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr3:146244800-146254600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr3:146244800-146258200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr3:146246600-146257200	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr3:146246800-146254600	Weak transcription	HepG2	liver
39	chr3:146247200-146254400	Weak transcription	Colon Smooth Muscle	Colon
40	chr3:146247200-146254400	Weak transcription	Stomach Smooth Muscle	stomach
41	chr3:146247200-146260800	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr3:146247400-146254400	Weak transcription	Ovary	ovary
43	chr3:146247800-146254400	Weak transcription	Fetal Stomach	stomach
44	chr3:146248800-146260800	Weak transcription	HSMM	muscle
45	chr3:146249000-146254600	Weak transcription	K562	blood
46	chr3:146249000-146259600	Weak transcription	Aorta	Aorta
47	chr3:146249200-146254400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr3:146249200-146254400	Weak transcription	Fetal Intestine Small	intestine
49	chr3:146249200-146254400	Weak transcription	Right Atrium	heart
50	chr3:146249400-146260800	Weak transcription	NHLF	lung

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