Variant report

Variant	rs2587013
Chromosome Location	chr3:146258609-146258610
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RELA	chr3:146257848-146258996	GM12878	blood:	n/a	chr3:146258206-146258215 chr3:146258206-146258215
2	POLR2A	chr3:146257555-146263098	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr3:146257006-146262899	K562	blood:	n/a	n/a
4	RELA	chr3:146257901-146258953	GM19099	blood:	n/a	chr3:146258206-146258215 chr3:146258206-146258215
5	E2F4	chr3:146258485-146258675	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:146246208..146248631-chr3:146255934..146259018,3	K562	blood:
2	chr3:146185784..146189530-chr3:146255597..146259009,4	K562	blood:
3	chr3:146254216..146256622-chr3:146257349..146260200,2	K562	blood:
4	chr3:146257059..146260785-chr3:146260976..146263871,3	MCF-7	breast:
5	chr3:146257750..146260238-chr3:146260636..146263970,4	K562	blood:

Variant related genes	Relation type
PLSCR1	TF binding region
ENSG00000188313	Chromatin interaction
ENSG00000163746	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1057481	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1061307	0.84[YRI][hapmap]
rs1079369	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13064509	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13069082	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1373246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1443827	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs16858420	1.00[JPT][hapmap];0.89[YRI][hapmap]
rs1882971	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1882972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1882973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1882974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1997601	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1997604	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2120381	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2165948	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2587007	0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2587008	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2587009	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2587010	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2587011	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2587012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2587014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2587015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2587016	1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2587017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2587018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2587021	0.91[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2587023	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2587024	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2609858	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs2609860	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2609861	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2609862	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609865	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609867	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688688	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2738905	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2738906	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2738907	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2738910	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2738911	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2738912	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2738915	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2738916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2738918	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2738920	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2738921	0.82[JPT][hapmap]
rs2738923	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35214899	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35309521	0.80[ASN][1000 genomes]
rs3773510	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3773521	0.86[CHB][hapmap]
rs67703040	0.84[ASN][1000 genomes]
rs7615988	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9289722	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs977758	0.86[ASN][1000 genomes]
rs9815834	0.86[CHB][hapmap]
rs9861142	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9865918	0.88[ASN][1000 genomes]
rs9876886	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv1014493	chr3:146255594-146288414	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:146225400-146260800	Weak transcription	NH-A	brain
2	chr3:146229000-146259600	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr3:146231600-146259000	Weak transcription	Brain Angular Gyrus	brain
4	chr3:146231600-146260800	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr3:146232000-146259600	Weak transcription	NHDF-Ad	bronchial
6	chr3:146233000-146259800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:146233000-146261400	Weak transcription	Fetal Muscle Trunk	muscle
8	chr3:146233600-146259200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr3:146247200-146260800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:146248800-146260800	Weak transcription	HSMM	muscle
11	chr3:146249000-146259600	Weak transcription	Aorta	Aorta
12	chr3:146249400-146260800	Weak transcription	NHLF	lung
13	chr3:146250600-146259600	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr3:146250600-146260000	Weak transcription	Thymus	Thymus
15	chr3:146250600-146260800	Weak transcription	Fetal Kidney	kidney
16	chr3:146251000-146259200	Weak transcription	Osteobl	bone
17	chr3:146251600-146259600	Weak transcription	Colonic Mucosa	Colon
18	chr3:146252600-146258800	Weak transcription	NHEK	skin
19	chr3:146252600-146259600	Weak transcription	Psoas Muscle	Psoas
20	chr3:146253400-146259200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr3:146254600-146259600	Weak transcription	HMEC	breast
22	chr3:146254600-146261400	Weak transcription	Brain Germinal Matrix	brain
23	chr3:146254800-146259600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr3:146254800-146259800	Weak transcription	Fetal Muscle Leg	muscle
25	chr3:146255000-146259000	Weak transcription	Stomach Smooth Muscle	stomach
26	chr3:146255000-146259400	Weak transcription	Fetal Lung	lung
27	chr3:146255000-146261000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr3:146255200-146258800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr3:146255200-146259800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:146255200-146260800	Weak transcription	Placenta	Placenta
31	chr3:146255400-146258800	Weak transcription	Colon Smooth Muscle	Colon
32	chr3:146255400-146259200	Weak transcription	Fetal Stomach	stomach
33	chr3:146255400-146259400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr3:146255400-146260800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr3:146255800-146259200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
36	chr3:146256000-146258800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:146256000-146259200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr3:146257000-146258800	Enhancers	Fetal Heart	heart
39	chr3:146257000-146259800	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr3:146257000-146260800	Enhancers	HepG2	liver
41	chr3:146257200-146258800	Enhancers	Adipose Nuclei	Adipose
42	chr3:146257200-146259400	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr3:146257200-146261000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr3:146257200-146261000	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr3:146257200-146261200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr3:146257400-146258800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr3:146257400-146259000	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr3:146257400-146259400	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr3:146257400-146259600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr3:146257400-146259600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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