Variant report

Variant	rs3777468
Chromosome Location	chr6:131483839-131483840
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:131482888..131484884-chr6:131488327..131490881,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10214430	0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10484764	1.00[AFR][1000 genomes]
rs12526166	1.00[AFR][1000 genomes]
rs12660246	1.00[AFR][1000 genomes]
rs12662825	1.00[AFR][1000 genomes]
rs12662942	0.80[CHB][hapmap];1.00[AMR][1000 genomes]
rs12664060	1.00[AFR][1000 genomes]
rs12665724	0.95[ASN][1000 genomes]
rs1569196	0.81[CHB][hapmap]
rs17060063	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs17060068	1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs17060099	1.00[AFR][1000 genomes]
rs17060119	1.00[AFR][1000 genomes]
rs2224637	1.00[AFR][1000 genomes]
rs2761285	0.93[ASN][1000 genomes]
rs3756773	1.00[AFR][1000 genomes]
rs3777469	1.00[AFR][1000 genomes]
rs3777470	1.00[AFR][1000 genomes]
rs3777473	1.00[AFR][1000 genomes]
rs3777479	1.00[AFR][1000 genomes]
rs3777481	1.00[AFR][1000 genomes]
rs3777482	1.00[AFR][1000 genomes]
rs3777484	1.00[AFR][1000 genomes]
rs3777498	1.00[AFR][1000 genomes]
rs3777499	1.00[AFR][1000 genomes]
rs3822867	1.00[AFR][1000 genomes]
rs589613	0.84[ASN][1000 genomes]
rs73633154	0.93[ASN][1000 genomes]
rs7772245	0.82[CHB][hapmap]
rs9483224	1.00[CHB][hapmap];0.84[JPT][hapmap];0.95[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	nsv1032955	chr6:131298803-131818502	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv538443	chr6:131298803-131818502	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv830807	chr6:131390952-131581931	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv886664	chr6:131443843-131754930	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131457200-131493400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr6:131457200-131504400	Weak transcription	Spleen	Spleen
3	chr6:131457600-131505600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr6:131457600-131520800	Weak transcription	Right Ventricle	heart
5	chr6:131457800-131486800	Weak transcription	Primary B cells from cord blood	blood
6	chr6:131457800-131487800	Weak transcription	Psoas Muscle	Psoas
7	chr6:131457800-131504200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr6:131457800-131504200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr6:131458000-131485400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr6:131458000-131487000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr6:131458000-131498800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr6:131458000-131505600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr6:131458000-131505800	Weak transcription	Duodenum Mucosa	Duodenum
14	chr6:131458200-131486600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr6:131458200-131505200	Weak transcription	Fetal Lung	lung
16	chr6:131458200-131513400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr6:131458400-131484800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr6:131458400-131485000	Weak transcription	Brain Angular Gyrus	brain
19	chr6:131458400-131498000	Weak transcription	Aorta	Aorta
20	chr6:131458400-131504200	Weak transcription	Dnd41	blood
21	chr6:131461200-131494600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr6:131461400-131485400	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr6:131463600-131484800	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr6:131464000-131484600	Weak transcription	Brain Hippocampus Middle	brain
25	chr6:131464000-131499200	Weak transcription	Fetal Stomach	stomach
26	chr6:131464200-131486600	Weak transcription	Fetal Muscle Trunk	muscle
27	chr6:131464600-131485000	Weak transcription	Brain Anterior Caudate	brain
28	chr6:131464800-131499200	Weak transcription	Esophagus	oesophagus
29	chr6:131467000-131485000	Weak transcription	Fetal Intestine Small	intestine
30	chr6:131467800-131486600	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr6:131468000-131486400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr6:131468200-131499800	Weak transcription	Lung	lung
33	chr6:131469000-131486800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr6:131469200-131504200	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr6:131469400-131485000	Weak transcription	Brain Substantia Nigra	brain
36	chr6:131479800-131484000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr6:131481200-131494600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr6:131481200-131504400	Weak transcription	HSMM	muscle
39	chr6:131481400-131485000	Weak transcription	Osteobl	bone
40	chr6:131481400-131486800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr6:131481600-131484800	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr6:131481600-131485200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr6:131481600-131485800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr6:131481800-131484800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr6:131481800-131485400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr6:131482000-131484800	Weak transcription	HepG2	liver
47	chr6:131482000-131485000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr6:131482200-131484600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr6:131482200-131486000	Weak transcription	Adipose Nuclei	Adipose
50	chr6:131482600-131485200	Weak transcription	Fetal Intestine Large	intestine

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