Variant report

Variant	rs2058325
Chromosome Location	chr6:29582629-29582630
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:29571256..29575251-chr6:29575309..29583536,9	K562	blood:
2	chr6:29581580..29583607-chr6:29588626..29591025,2	K562	blood:
3	chr6:29578909..29580835-chr6:29582417..29583981,2	K562	blood:
4	chr6:29581672..29583351-chr6:29584179..29587675,3	K562	blood:
5	chr6:29578000..29583607-chr6:29584816..29592316,14	K562	blood:
6	chr6:29573160..29575251-chr6:29581192..29583536,2	K562	blood:
7	chr6:29579403..29583874-chr6:29593619..29596165,4	K562	blood:

Variant related genes	Relation type
ENSG00000204681	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs16895101	0.82[ASN][1000 genomes]
rs2057010	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2058326	0.95[ASN][1000 genomes]
rs28359971	0.90[ASN][1000 genomes]
rs28359972	0.92[ASN][1000 genomes]
rs28749524	0.92[ASN][1000 genomes]
rs29219	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs29256	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs29266	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3025628	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3025642	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs362515	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs362517	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55701059	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55871431	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55888673	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55971964	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56020557	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56045105	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56106029	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56142919	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56155438	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56393713	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62392941	0.91[ASN][1000 genomes]
rs62392942	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62392943	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62392944	0.92[EUR][1000 genomes]
rs62406580	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62406582	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62406583	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62406584	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72831507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758039	chr6:29469101-29672665	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv2759411	chr6:29469101-29672665	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv528285	chr6:29566842-29588146	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv462671	chr6:29566842-29588146	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv601229	chr6:29566842-29588146	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29566400-29595200	Weak transcription	Right Atrium	heart
2	chr6:29566600-29587000	Strong transcription	Primary neutrophils fromperipheralblood	blood
3	chr6:29566800-29584600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr6:29566800-29590000	Strong transcription	H9 Cell Line	embryonic stem cell
5	chr6:29566800-29590600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr6:29567000-29589800	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr6:29567200-29589400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr6:29567200-29589800	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr6:29567600-29583800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr6:29567600-29592400	Strong transcription	Fetal Stomach	stomach
11	chr6:29567600-29595400	Weak transcription	A549	lung
12	chr6:29567800-29582800	Strong transcription	Ovary	ovary
13	chr6:29567800-29584600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:29568400-29583600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr6:29568600-29595200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr6:29568800-29583200	Strong transcription	NHEK	skin
17	chr6:29569000-29582800	Strong transcription	Osteobl	bone
18	chr6:29569000-29584600	Strong transcription	Spleen	Spleen
19	chr6:29569000-29592400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr6:29569200-29582800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr6:29569200-29592200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr6:29569400-29592000	Strong transcription	Stomach Smooth Muscle	stomach
23	chr6:29569400-29595600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr6:29569800-29583000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr6:29569800-29583200	Strong transcription	Fetal Muscle Trunk	muscle
26	chr6:29570800-29589600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr6:29571400-29583200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:29571400-29584400	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr6:29571600-29582800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr6:29571600-29589800	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr6:29572000-29583200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr6:29572000-29590000	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr6:29572200-29588800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr6:29572200-29595600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr6:29572400-29592000	Strong transcription	Fetal Brain Female	brain
36	chr6:29572400-29593000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr6:29572600-29583000	Strong transcription	Brain Germinal Matrix	brain
38	chr6:29572800-29586000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
39	chr6:29573000-29591000	Weak transcription	Duodenum Mucosa	Duodenum
40	chr6:29574400-29595400	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr6:29574800-29595000	Weak transcription	Pancreas	Pancrea
42	chr6:29575000-29583400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
43	chr6:29575200-29588800	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr6:29575200-29590800	Weak transcription	Primary T cells from cord blood	blood
45	chr6:29575400-29591600	Weak transcription	Colonic Mucosa	Colon
46	chr6:29575600-29587000	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr6:29576200-29588200	Weak transcription	Rectal Smooth Muscle	rectum
48	chr6:29576400-29588400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr6:29576800-29589600	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr6:29576800-29589800	Weak transcription	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links