Variant report

Variant	rs57573658
Chromosome Location	chr6:88381358-88381359
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:88377817..88379372-chr6:88381342..88384204,2	K562	blood:
2	chr6:88381197..88391198-chr6:88407466..88413401,14	K562	blood:
3	chr6:88365678..88369337-chr6:88379834..88383154,3	K562	blood:
4	chr6:88377297..88379434-chr6:88381335..88385575,5	K562	blood:
5	chr6:88374136..88375947-chr6:88380519..88382836,2	K562	blood:
6	chr6:88379359..88381914-chr6:88410381..88412364,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135334	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs16879704	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs28381530	1.00[ASN][1000 genomes]
rs3763177	0.94[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs41273297	0.91[ASN][1000 genomes]
rs55909105	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55985738	0.91[ASN][1000 genomes]
rs56400749	0.91[ASN][1000 genomes]
rs58060521	0.91[AFR][1000 genomes]
rs59774543	0.91[ASN][1000 genomes]
rs60082015	0.91[ASN][1000 genomes]
rs60316099	0.91[ASN][1000 genomes]
rs66502414	0.91[ASN][1000 genomes]
rs66965134	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs67993159	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs68082038	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6907107	0.91[ASN][1000 genomes]
rs6932733	0.86[ASN][1000 genomes]
rs715207	0.97[ASN][1000 genomes]
rs72924341	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72924342	0.91[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs73498106	0.91[ASN][1000 genomes]
rs7747792	0.91[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7752473	0.91[ASN][1000 genomes]
rs7769144	0.91[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	nsv1031460	chr6:88153079-88410050	Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv1026482	chr6:88164934-88409728	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1027706	chr6:88168987-88409728	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	esv2758068	chr6:88358988-88441473	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	esv2759454	chr6:88358988-88441473	Strong transcription Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88300600-88391200	Weak transcription	Colonic Mucosa	Colon
2	chr6:88301200-88385000	Weak transcription	Colon Smooth Muscle	Colon
3	chr6:88305000-88398800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr6:88314000-88384800	Weak transcription	Hela-S3	cervix
5	chr6:88314200-88399200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr6:88314600-88385000	Weak transcription	Esophagus	oesophagus
7	chr6:88316600-88390000	Weak transcription	Pancreas	Pancrea
8	chr6:88320400-88400800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr6:88322800-88382000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr6:88324000-88385000	Weak transcription	Gastric	stomach
11	chr6:88329800-88383200	Weak transcription	Lung	lung
12	chr6:88333400-88384800	Weak transcription	Brain Angular Gyrus	brain
13	chr6:88339200-88396800	Weak transcription	Right Ventricle	heart
14	chr6:88344400-88384800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr6:88348000-88385000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr6:88349200-88381400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr6:88349400-88385000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr6:88349400-88397400	Weak transcription	Ovary	ovary
19	chr6:88358200-88392000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:88363000-88408200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr6:88363200-88395000	Weak transcription	Stomach Mucosa	stomach
22	chr6:88364400-88384800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr6:88365000-88390000	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr6:88366400-88390000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr6:88366600-88390000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr6:88367800-88385000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr6:88368000-88382000	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr6:88368000-88393400	Weak transcription	Small Intestine	intestine
29	chr6:88370200-88391800	Weak transcription	Fetal Brain Male	brain
30	chr6:88370400-88381400	Weak transcription	HUVEC	blood vessel
31	chr6:88370400-88384800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr6:88371000-88381800	Weak transcription	Rectal Smooth Muscle	rectum
33	chr6:88371000-88383000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr6:88371400-88381800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr6:88371600-88383400	Weak transcription	Psoas Muscle	Psoas
36	chr6:88371600-88385000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr6:88372600-88392000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr6:88372800-88383000	Weak transcription	Fetal Stomach	stomach
39	chr6:88374200-88391400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr6:88374800-88382200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr6:88374800-88382200	Weak transcription	K562	blood
42	chr6:88375600-88384800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr6:88376200-88385800	Strong transcription	HSMM	muscle
44	chr6:88376400-88390000	Strong transcription	Primary B cells from cord blood	blood
45	chr6:88376600-88384800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr6:88376600-88390000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr6:88376800-88384600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr6:88376800-88389400	Strong transcription	Fetal Muscle Trunk	muscle
49	chr6:88376800-88389800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr6:88377000-88383200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links