Variant report

Variant	rs4688043
Chromosome Location	chr3:119591248-119591249
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119590590..119592334-chr3:119593931..119596486,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000082701	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1154596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1154597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11921053	0.91[ASN][1000 genomes]
rs13312998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13314595	1.00[CHB][hapmap]
rs1579031	0.84[ASN][1000 genomes]
rs1626696	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16830683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16830689	1.00[CHB][hapmap]
rs1719887	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs1719888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1719889	1.00[CHB][hapmap]
rs1719895	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1732165	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1732169	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs182839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2037547	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2461816	0.82[CHB][hapmap]
rs2461827	1.00[ASN][1000 genomes]
rs2472680	0.82[CHB][hapmap]
rs28516957	0.84[ASN][1000 genomes]
rs3108749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs334534	0.88[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs334536	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs334551	0.88[EUR][1000 genomes]
rs334552	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs334554	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs334560	0.85[ASN][1000 genomes]
rs334561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs334566	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs3853592	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4072520	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs4438691	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4605584	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60272712	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6438550	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6438554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6438555	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs66650215	0.94[ASN][1000 genomes]
rs6762640	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6769435	1.00[CHB][hapmap]
rs6770314	1.00[CHB][hapmap]
rs6771023	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6774693	0.91[ASN][1000 genomes]
rs6779828	1.00[CHB][hapmap]
rs6784239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6785050	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6790751	1.00[CHB][hapmap]
rs6797689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6797879	0.86[AFR][1000 genomes]
rs6805931	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6807868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7617372	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs7620750	0.82[CHB][hapmap];0.84[ASN][1000 genomes]
rs7624540	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7628426	0.88[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7635604	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7636600	0.91[ASN][1000 genomes]
rs7650554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7652172	1.00[CHB][hapmap]
rs968824	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9784393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9829763	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9851174	1.00[CHB][hapmap]
rs9859778	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9879992	1.00[CHB][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	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv829696	chr3:119567659-119711405	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119546000-119663400	Weak transcription	Lung	lung
2	chr3:119551400-119594600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:119562400-119611000	Weak transcription	Fetal Stomach	stomach
4	chr3:119567000-119605200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr3:119569400-119629400	Weak transcription	Esophagus	oesophagus
6	chr3:119574600-119631600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:119577000-119598800	Weak transcription	Fetal Brain Male	brain
8	chr3:119577400-119596600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:119577600-119598200	Weak transcription	Left Ventricle	heart
10	chr3:119577600-119602800	Weak transcription	Psoas Muscle	Psoas
11	chr3:119577600-119607600	Weak transcription	Aorta	Aorta
12	chr3:119577800-119607600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:119578000-119601400	Weak transcription	Fetal Intestine Small	intestine
14	chr3:119581800-119605400	Weak transcription	Colonic Mucosa	Colon
15	chr3:119582400-119591800	Weak transcription	Placenta	Placenta
16	chr3:119582400-119593600	Weak transcription	Fetal Lung	lung
17	chr3:119582400-119596800	Weak transcription	Fetal Kidney	kidney
18	chr3:119582400-119598400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:119582400-119602200	Weak transcription	A549	lung
20	chr3:119582400-119607400	Weak transcription	Ovary	ovary
21	chr3:119582400-119607600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr3:119582400-119607600	Weak transcription	Fetal Brain Female	brain
23	chr3:119582400-119607600	Weak transcription	Thymus	Thymus
24	chr3:119582400-119607800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr3:119582400-119610600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr3:119582400-119610600	Weak transcription	Colon Smooth Muscle	Colon
27	chr3:119582400-119611000	Weak transcription	Brain Anterior Caudate	brain
28	chr3:119582400-119611000	Weak transcription	Brain Cingulate Gyrus	brain
29	chr3:119582400-119611000	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr3:119582400-119611000	Weak transcription	HUVEC	blood vessel
31	chr3:119582400-119624000	Weak transcription	Brain Germinal Matrix	brain
32	chr3:119582400-119626600	Weak transcription	Fetal Heart	heart
33	chr3:119582400-119629400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr3:119582600-119592000	Weak transcription	Primary hematopoietic stem cells	blood
35	chr3:119582600-119594400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr3:119582600-119594400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr3:119582600-119595000	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr3:119582600-119595600	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr3:119582600-119598400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr3:119582600-119598400	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr3:119582600-119598800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr3:119582600-119599000	Weak transcription	NH-A	brain
43	chr3:119582600-119602000	Weak transcription	Hela-S3	cervix
44	chr3:119582600-119602400	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr3:119582600-119602400	Weak transcription	Fetal Muscle Leg	muscle
46	chr3:119582600-119602400	Weak transcription	HSMMtube	muscle
47	chr3:119582600-119602800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr3:119582600-119607600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr3:119582600-119607800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr3:119582600-119609800	Weak transcription	Rectal Smooth Muscle	rectum

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