Variant report

Variant	rs6775397
Chromosome Location	chr3:119661373-119661374
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119659377..119662242-chr3:119664934..119667462,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10934503	0.81[YRI][hapmap]
rs10934506	0.83[YRI][hapmap]
rs11915717	0.83[YRI][hapmap]
rs11921053	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12494560	0.84[AMR][1000 genomes]
rs13314595	0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1579031	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16830689	0.84[YRI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1719889	0.84[YRI][hapmap];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2037547	0.80[AMR][1000 genomes]
rs2461827	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28516957	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs334535	0.82[YRI][hapmap];0.82[EUR][1000 genomes]
rs334536	0.81[EUR][1000 genomes]
rs334559	0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs334560	0.81[EUR][1000 genomes]
rs334566	0.81[EUR][1000 genomes]
rs4072520	0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4340737	0.83[YRI][hapmap]
rs4450859	0.92[AMR][1000 genomes]
rs4624596	0.83[YRI][hapmap]
rs4688042	0.83[YRI][hapmap]
rs4688046	0.83[YRI][hapmap]
rs4688047	0.83[YRI][hapmap]
rs4688054	0.83[YRI][hapmap]
rs56126162	0.84[AMR][1000 genomes]
rs58043853	0.80[EUR][1000 genomes]
rs6438555	0.81[EUR][1000 genomes]
rs66650215	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6769435	0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6770314	0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6771023	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6774693	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6779828	0.87[YRI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6790751	0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs6795874	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6802301	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7613197	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7617372	0.82[YRI][hapmap];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7620750	0.95[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7624540	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7636600	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7649661	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7652172	0.91[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9289138	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs968824	0.81[EUR][1000 genomes]
rs9851174	0.82[YRI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9859778	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9879992	1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.85[EUR][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	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:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119546000-119663400	Weak transcription	Lung	lung
2	chr3:119608200-119677800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr3:119611200-119667000	Weak transcription	Pancreas	Pancrea
4	chr3:119611400-119682200	Weak transcription	HSMMtube	muscle
5	chr3:119625000-119668200	Weak transcription	Hela-S3	cervix
6	chr3:119628200-119663200	Weak transcription	Right Atrium	heart
7	chr3:119629600-119672200	Weak transcription	Fetal Stomach	stomach
8	chr3:119630800-119663200	Weak transcription	Esophagus	oesophagus
9	chr3:119630800-119697400	Weak transcription	Thymus	Thymus
10	chr3:119631000-119717000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:119635000-119665400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr3:119635000-119667000	Weak transcription	Placenta	Placenta
13	chr3:119635400-119664600	Weak transcription	HMEC	breast
14	chr3:119636400-119667200	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr3:119640000-119663800	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr3:119640600-119664400	Weak transcription	HSMM	muscle
17	chr3:119640600-119665000	Weak transcription	Primary B cells from peripheral blood	blood
18	chr3:119640600-119672400	Weak transcription	Osteobl	bone
19	chr3:119640800-119665400	Weak transcription	Fetal Thymus	thymus
20	chr3:119641000-119661800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:119641000-119662600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr3:119641000-119663800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:119641000-119681600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr3:119641000-119681600	Weak transcription	Fetal Intestine Small	intestine
25	chr3:119641000-119694400	Weak transcription	Fetal Lung	lung
26	chr3:119641200-119664400	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr3:119641200-119666400	Weak transcription	HepG2	liver
28	chr3:119641200-119681200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr3:119642200-119665600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr3:119645400-119669600	Weak transcription	Psoas Muscle	Psoas
31	chr3:119650200-119669800	Weak transcription	Liver	Liver
32	chr3:119650400-119669600	Weak transcription	Left Ventricle	heart
33	chr3:119653400-119661600	Weak transcription	NHDF-Ad	bronchial
34	chr3:119653600-119669600	Weak transcription	Ovary	ovary
35	chr3:119656200-119663400	Weak transcription	Duodenum Mucosa	Duodenum
36	chr3:119656400-119662200	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr3:119656400-119662400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr3:119656400-119663200	Weak transcription	Primary B cells from cord blood	blood
39	chr3:119656400-119663200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr3:119656400-119669400	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr3:119656400-119680600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr3:119656400-119681200	Weak transcription	Primary hematopoietic stem cells	blood
43	chr3:119656400-119700000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr3:119656600-119661800	Weak transcription	Rectal Smooth Muscle	rectum
45	chr3:119656600-119663200	Weak transcription	Primary T cells from cord blood	blood
46	chr3:119656600-119664200	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr3:119656600-119669800	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr3:119656600-119718400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr3:119657000-119663400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr3:119657200-119663200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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