Variant report

Variant	rs3777484
Chromosome Location	chr6:131579434-131579435
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:131574679..131577194-chr6:131577773..131580608,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10484763	1.00[JPT][hapmap]
rs10484764	0.91[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1190802	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1190810	0.80[ASN][1000 genomes]
rs1190812	0.80[ASN][1000 genomes]
rs12525492	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12526166	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12660246	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12662825	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12664060	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1322596	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17060063	1.00[AFR][1000 genomes]
rs17060068	1.00[AFR][1000 genomes]
rs17060099	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17060119	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17060127	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1746469	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2224637	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28841032	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3756773	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3777468	1.00[AFR][1000 genomes]
rs3777469	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3777470	0.91[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3777471	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3777473	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3777474	0.80[ASN][1000 genomes]
rs3777477	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs3777479	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3777481	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3777482	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3777491	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3777495	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3777496	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3777497	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3777498	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3777499	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3822867	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4596509	0.81[ASN][1000 genomes]
rs9375802	1.00[EUR][1000 genomes]
rs9492888	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9492889	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
5	nsv886665	chr6:131518894-131611309	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv830808	chr6:131521115-131735320	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
7	esv1835599	chr6:131554291-131590766	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv886666	chr6:131573433-131666295	Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131563000-131580000	Weak transcription	Small Intestine	intestine
2	chr6:131571800-131580000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr6:131571800-131583000	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr6:131571800-131583200	Weak transcription	Aorta	Aorta
5	chr6:131571800-131587200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr6:131571800-131591400	Weak transcription	Psoas Muscle	Psoas
7	chr6:131571800-131592600	Weak transcription	Fetal Thymus	thymus
8	chr6:131571800-131596800	Weak transcription	Lung	lung
9	chr6:131571800-131603000	Weak transcription	Esophagus	oesophagus
10	chr6:131571800-131614400	Weak transcription	Gastric	stomach
11	chr6:131572200-131613000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr6:131572600-131587000	Weak transcription	Brain Substantia Nigra	brain
13	chr6:131573000-131590600	Weak transcription	Adipose Nuclei	Adipose
14	chr6:131573400-131580000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr6:131573400-131584200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr6:131573400-131591200	Weak transcription	Liver	Liver
17	chr6:131573600-131579600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr6:131573600-131590400	Weak transcription	Left Ventricle	heart
19	chr6:131573600-131610400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr6:131573800-131580000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:131573800-131590200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr6:131574000-131590400	Weak transcription	Brain Anterior Caudate	brain
23	chr6:131574200-131601600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr6:131574200-131601600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr6:131574400-131591000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr6:131575600-131602400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:131576200-131581200	Enhancers	Fetal Intestine Large	intestine
28	chr6:131576600-131581000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr6:131577000-131591400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr6:131577000-131601600	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr6:131577200-131580200	Weak transcription	Fetal Heart	heart
32	chr6:131577200-131590200	Weak transcription	Fetal Stomach	stomach
33	chr6:131577400-131580200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr6:131577400-131581000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr6:131577400-131581000	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr6:131577400-131582800	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr6:131577400-131590400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr6:131577400-131590400	Weak transcription	Fetal Muscle Leg	muscle
39	chr6:131577400-131590800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr6:131577400-131601400	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr6:131577600-131580200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr6:131577800-131580000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr6:131577800-131580400	Enhancers	Fetal Intestine Small	intestine
44	chr6:131578400-131580600	Enhancers	Fetal Kidney	kidney
45	chr6:131578600-131580200	Enhancers	HepG2	liver
46	chr6:131578800-131580000	Weak transcription	Colonic Mucosa	Colon
47	chr6:131578800-131580600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr6:131578800-131580600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr6:131578800-131590400	Weak transcription	Fetal Lung	lung
50	chr6:131579000-131579800	Enhancers	A549	lung

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