Variant report

Variant	rs3778513
Chromosome Location	chr6:57180693-57180694
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56818167..56820292-chr6:57177596..57182762,4	MCF-7	breast:
2	chr6:56818015..56821855-chr6:57180367..57183028,4	K562	blood:
3	chr6:57084710..57087719-chr6:57179458..57182091,4	MCF-7	breast:
4	chr6:57177396..57179187-chr6:57179972..57181489,2	K562	blood:

Variant related genes	Relation type
ENSG00000151914	Chromatin interaction
ENSG00000151917	Chromatin interaction
ENSG00000112210	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs12180921	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1476852	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1741910	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1741911	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1741912	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1741913	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1741915	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1755831	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1755832	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1755834	1.00[CEU][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]
rs17705499	0.89[YRI][hapmap]
rs1860652	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1888265	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1888266	1.00[CEU][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]
rs28367021	0.86[AFR][1000 genomes]
rs28800513	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3757295	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3778514	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800007	1.00[JPT][hapmap]
rs3800010	1.00[JPT][hapmap]
rs3800014	1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[ASN][1000 genomes]
rs3800016	1.00[JPT][hapmap];0.89[YRI][hapmap]
rs4615395	0.94[YRI][hapmap]
rs4712146	0.89[YRI][hapmap]
rs4715652	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4992408	0.90[YRI][hapmap]
rs58482037	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs58651731	1.00[ASN][1000 genomes]
rs59431929	1.00[ASN][1000 genomes]
rs6459186	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6459188	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911273	1.00[ASN][1000 genomes]
rs6911353	1.00[JPT][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6915533	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6916106	0.93[EUR][1000 genomes]
rs6936450	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6938582	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7754911	0.86[AFR][1000 genomes]
rs9296875	1.00[JPT][hapmap]
rs9396273	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9396274	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9464433	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs9464434	1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9464437	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9464438	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9464440	1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[ASN][1000 genomes]
rs9475820	1.00[ASN][1000 genomes]
rs9475837	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9475840	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9475841	0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9475842	0.86[AFR][1000 genomes]
rs9475844	0.90[YRI][hapmap];0.86[AFR][1000 genomes]
rs9475845	1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9475847	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9475852	1.00[ASN][1000 genomes]
rs9475856	1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[ASN][1000 genomes]
rs9475861	1.00[JPT][hapmap];0.88[YRI][hapmap]
rs9475862	0.87[ASN][1000 genomes]
rs9475863	1.00[ASN][1000 genomes]
rs9475882	1.00[JPT][hapmap]
rs9475887	1.00[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:57176800-57181200	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr6:57177000-57181200	Enhancers	NHDF-Ad	bronchial
3	chr6:57178600-57181200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr6:57178600-57181200	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr6:57178600-57181200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr6:57178600-57181200	Enhancers	HSMM	muscle
7	chr6:57178600-57181200	Enhancers	Osteobl	bone
8	chr6:57178600-57181600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr6:57178800-57181000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr6:57178800-57181200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:57178800-57181200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr6:57178800-57181200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr6:57178800-57181200	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr6:57178800-57181200	Weak transcription	Stomach Mucosa	stomach
15	chr6:57178800-57181200	Weak transcription	K562	blood
16	chr6:57178800-57181400	Weak transcription	Fetal Intestine Small	intestine
17	chr6:57178800-57181400	Weak transcription	Ovary	ovary
18	chr6:57178800-57181400	Enhancers	Rectal Smooth Muscle	rectum
19	chr6:57178800-57181600	Weak transcription	Esophagus	oesophagus
20	chr6:57179000-57181200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr6:57179000-57181200	Weak transcription	Fetal Kidney	kidney
22	chr6:57179000-57181200	Weak transcription	Fetal Lung	lung
23	chr6:57179000-57181200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr6:57179200-57181400	Weak transcription	Colonic Mucosa	Colon
25	chr6:57179200-57181400	Enhancers	Colon Smooth Muscle	Colon
26	chr6:57179200-57181600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr6:57179400-57181200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr6:57179400-57181200	Weak transcription	Fetal Muscle Leg	muscle
29	chr6:57179400-57181600	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr6:57179600-57181200	Weak transcription	Hela-S3	cervix
31	chr6:57179800-57181000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr6:57179800-57181000	Weak transcription	HUVEC	blood vessel
33	chr6:57179800-57181200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr6:57179800-57181200	Weak transcription	A549	lung
35	chr6:57179800-57181400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr6:57179800-57181400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr6:57179800-57181400	Weak transcription	Aorta	Aorta
38	chr6:57180000-57181000	Weak transcription	Fetal Stomach	stomach
39	chr6:57180000-57181000	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr6:57180000-57181400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr6:57180200-57181000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr6:57180200-57181200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr6:57180200-57181200	Weak transcription	NH-A	brain
44	chr6:57180200-57181200	Weak transcription	NHEK	skin
45	chr6:57180200-57181200	Weak transcription	NHLF	lung
46	chr6:57180400-57180800	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr6:57180400-57180800	Weak transcription	HMEC	breast
48	chr6:57180600-57181000	Enhancers	HepG2	liver
49	chr6:57180600-57181200	Weak transcription	HSMMtube	muscle

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