Variant report

Variant	rs3777498
Chromosome Location	chr6:131601825-131601826
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10484763	1.00[JPT][hapmap]
rs10484764	0.91[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1190802	1.00[JPT][hapmap]
rs12525492	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12526166	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12660246	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12662825	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12664060	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1322596	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17060063	1.00[AFR][1000 genomes]
rs17060068	1.00[AFR][1000 genomes]
rs17060099	0.91[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17060119	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17060127	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1746469	1.00[JPT][hapmap]
rs2224637	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]
rs28841032	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3756773	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3777468	1.00[AFR][1000 genomes]
rs3777469	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3777470	0.91[CHB][hapmap];0.94[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3777471	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3777473	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3777477	1.00[JPT][hapmap]
rs3777479	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3777481	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3777482	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3777484	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]
rs3777491	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3777495	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3777496	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3777497	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3777499	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3822867	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]
rs9375802	1.00[EUR][1000 genomes]
rs9492888	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9492889	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
4	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
5	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
6	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:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131571800-131603000	Weak transcription	Esophagus	oesophagus
2	chr6:131571800-131614400	Weak transcription	Gastric	stomach
3	chr6:131572200-131613000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:131573600-131610400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr6:131575600-131602400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr6:131580600-131602400	Weak transcription	Small Intestine	intestine
7	chr6:131580600-131602600	Weak transcription	Right Ventricle	heart
8	chr6:131580600-131606000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr6:131580800-131605000	Weak transcription	Fetal Heart	heart
10	chr6:131587400-131614400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr6:131587600-131602800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr6:131590800-131610200	Weak transcription	Fetal Stomach	stomach
13	chr6:131591000-131614800	Weak transcription	Fetal Muscle Trunk	muscle
14	chr6:131591200-131602600	Weak transcription	Left Ventricle	heart
15	chr6:131591200-131603000	Weak transcription	Aorta	Aorta
16	chr6:131591400-131610600	Weak transcription	Stomach Smooth Muscle	stomach
17	chr6:131591800-131602200	Weak transcription	Fetal Lung	lung
18	chr6:131591800-131602800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr6:131591800-131603400	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr6:131592000-131602200	Weak transcription	Primary B cells from cord blood	blood
21	chr6:131592000-131602200	Weak transcription	Fetal Intestine Small	intestine
22	chr6:131592000-131602600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr6:131592200-131602200	Weak transcription	Duodenum Mucosa	Duodenum
24	chr6:131594400-131602200	Weak transcription	Fetal Brain Female	brain
25	chr6:131596600-131602200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr6:131597000-131602600	Weak transcription	Lung	lung
27	chr6:131597200-131613200	Weak transcription	Ovary	ovary
28	chr6:131598000-131602200	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr6:131600000-131602400	Weak transcription	Fetal Intestine Large	intestine
30	chr6:131600400-131602200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr6:131601200-131602200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr6:131601200-131602400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr6:131601200-131602400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr6:131601200-131612000	Weak transcription	HSMMtube	muscle
35	chr6:131601400-131602400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr6:131601400-131602400	Enhancers	Primary T cells from cord blood	blood
37	chr6:131601400-131602400	Enhancers	Primary T cells fromperipheralblood	blood
38	chr6:131601400-131602400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr6:131601400-131602400	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr6:131601400-131602400	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr6:131601400-131602400	Enhancers	Brain Angular Gyrus	brain
42	chr6:131601400-131602600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr6:131601400-131602600	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr6:131601400-131602600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr6:131601400-131602800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr6:131601400-131602800	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr6:131601400-131603400	Enhancers	Fetal Brain Male	brain
48	chr6:131601400-131604400	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr6:131601600-131602000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr6:131601600-131602200	Enhancers	Brain Substantia Nigra	brain

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