Variant report

Variant	rs6905084
Chromosome Location	chr6:5003766-5003767
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	chr6:4776139..4778956-chr6:5002447..5004557,2	K562	blood:
2	chr6:5002773..5004480-chr6:5029318..5032794,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272142	Chromatin interaction
ENSG00000153046	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs11758411	0.81[EUR][1000 genomes]
rs11759046	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1417656	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1749154	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1749161	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1749165	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1771865	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1771866	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1771867	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1771871	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1886567	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2326574	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764102	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764103	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764104	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764105	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764106	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764107	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764108	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2764109	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764112	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764114	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764115	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764116	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764120	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764121	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764123	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764124	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764125	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764126	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764127	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2764129	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764130	1.00[ASN][1000 genomes]
rs2764132	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2764134	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764135	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764137	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764138	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764139	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764141	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764142	1.00[ASN][1000 genomes]
rs2764143	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764145	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764148	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2764149	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764151	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764152	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764166	1.00[ASN][1000 genomes]
rs2764169	1.00[ASN][1000 genomes]
rs2764185	0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2764186	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2764191	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764192	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2793240	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2793241	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2793242	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2793245	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2793247	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2793249	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2793250	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2793251	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2985675	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2994694	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34471690	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4960056	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5018030	0.90[AMR][1000 genomes]
rs62385141	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6912320	1.00[ASN][1000 genomes]
rs795809	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs795810	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs795811	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs912709	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs912710	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs912711	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs947153	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9502260	1.00[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	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2422499	chr6:4745428-5073222	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv830577	chr6:4834567-5050544	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv462622	chr6:4904380-5172009	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv600871	chr6:4904380-5172009	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv1033905	chr6:4955826-5080904	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv600872	chr6:4975313-5342190	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	nsv1031837	chr6:4996667-5418726	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5000600-5004000	Weak transcription	Fetal Brain Male	brain
2	chr6:5003000-5003800	Flanking Active TSS	Dnd41	blood
3	chr6:5003000-5004600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr6:5003000-5004800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr6:5003000-5005000	Active TSS	Brain Anterior Caudate	brain
6	chr6:5003200-5004400	Active TSS	Primary neutrophils fromperipheralblood	blood
7	chr6:5003200-5004400	Active TSS	Primary T helper cells fromperipheralblood	blood
8	chr6:5003200-5004400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:5003200-5004600	Active TSS	Brain Hippocampus Middle	brain
10	chr6:5003200-5004600	Active TSS	Duodenum Mucosa	Duodenum
11	chr6:5003200-5004600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
12	chr6:5003200-5004600	Active TSS	Hela-S3	cervix
13	chr6:5003200-5004600	Active TSS	Osteobl	bone
14	chr6:5003200-5004800	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr6:5003200-5004800	Active TSS	iPS-20b Cell Line	embryonic stem cell
16	chr6:5003200-5004800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr6:5003200-5004800	Active TSS	NHDF-Ad	bronchial
18	chr6:5003200-5004800	Active TSS	NHEK	skin
19	chr6:5003200-5005000	Active TSS	A549	lung
20	chr6:5003200-5005200	Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr6:5003200-5005200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr6:5003400-5003800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
23	chr6:5003400-5003800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr6:5003400-5003800	Flanking Active TSS	HepG2	liver
25	chr6:5003400-5003800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
26	chr6:5003400-5004000	Flanking Active TSS	Fetal Muscle Trunk	muscle
27	chr6:5003400-5004000	Flanking Active TSS	Placenta	Placenta
28	chr6:5003400-5004400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
29	chr6:5003400-5004400	Active TSS	Muscle Satellite Cultured Cells	--
30	chr6:5003400-5004400	Active TSS	Cortex derived primary cultured neurospheres	brain
31	chr6:5003400-5004400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr6:5003400-5004400	Active TSS	Colonic Mucosa	Colon
33	chr6:5003400-5004600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr6:5003400-5004600	Active TSS	Fetal Brain Female	brain
35	chr6:5003400-5004600	Active TSS	Fetal Intestine Large	intestine
36	chr6:5003400-5004600	Active TSS	Rectal Mucosa Donor 31	rectum
37	chr6:5003400-5004600	Active TSS	GM12878-XiMat	blood
38	chr6:5003400-5004600	Active TSS	NH-A	brain
39	chr6:5003400-5004800	Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr6:5003400-5004800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr6:5003400-5004800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr6:5003400-5004800	Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr6:5003400-5004800	Active TSS	HSMM	muscle
44	chr6:5003400-5005200	Active TSS	Psoas Muscle	Psoas
45	chr6:5003600-5003800	Flanking Active TSS	H1 Cell Line	embryonic stem cell
46	chr6:5003600-5003800	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr6:5003600-5003800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr6:5003600-5003800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr6:5003600-5003800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr6:5003600-5003800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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