Variant report

Variant	rs542056
Chromosome Location	chr6:33577084-33577085
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:33576666..33582891-chr6:33586745..33591603,10	MCF-7	breast:
2	chr6:33576269..33579262-chr6:33600060..33601906,2	MCF-7	breast:
3	chr6:33555689..33557372-chr6:33575674..33577429,2	MCF-7	breast:
4	chr6:33574216..33577618-chr6:33579266..33582393,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000096433	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1536042	1.00[ASN][1000 genomes]
rs16869178	1.00[ASN][1000 genomes]
rs1755041	1.00[ASN][1000 genomes]
rs1755042	1.00[ASN][1000 genomes]
rs1755054	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1794686	1.00[ASN][1000 genomes]
rs1794688	1.00[ASN][1000 genomes]
rs2068236	1.00[ASN][1000 genomes]
rs2147655	1.00[ASN][1000 genomes]
rs2395451	1.00[ASN][1000 genomes]
rs4711333	1.00[ASN][1000 genomes]
rs4711334	1.00[ASN][1000 genomes]
rs4711335	0.81[AMR][1000 genomes]
rs4713647	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4713652	1.00[ASN][1000 genomes]
rs472990	1.00[ASN][1000 genomes]
rs480568	1.00[ASN][1000 genomes]
rs485623	1.00[ASN][1000 genomes]
rs535584	1.00[ASN][1000 genomes]
rs542725	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs549719	0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55700437	1.00[ASN][1000 genomes]
rs557559	1.00[ASN][1000 genomes]
rs560218	1.00[ASN][1000 genomes]
rs561276	1.00[ASN][1000 genomes]
rs572824	1.00[ASN][1000 genomes]
rs6906810	1.00[ASN][1000 genomes]
rs71536195	1.00[ASN][1000 genomes]
rs7752930	1.00[ASN][1000 genomes]
rs7757391	1.00[ASN][1000 genomes]
rs7757722	1.00[ASN][1000 genomes]
rs7759154	1.00[ASN][1000 genomes]
rs7775313	1.00[ASN][1000 genomes]
rs806604	1.00[ASN][1000 genomes]
rs9368770	1.00[ASN][1000 genomes]
rs9689326	1.00[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	nsv462896	chr6:33534880-33588147	Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv602833	chr6:33534880-33588147	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv885770	chr6:33543409-33614127	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv830638	chr6:33551202-33711346	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
5	nsv5250	chr6:33565017-33598370	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33571600-33579000	Enhancers	Placenta	Placenta
2	chr6:33573400-33577200	Weak transcription	Fetal Intestine Large	intestine
3	chr6:33573400-33577600	Weak transcription	Colonic Mucosa	Colon
4	chr6:33574400-33578600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:33574400-33579000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr6:33574400-33579400	Enhancers	Spleen	Spleen
7	chr6:33574400-33579600	Enhancers	H1 Cell Line	embryonic stem cell
8	chr6:33574400-33579600	Enhancers	Stomach Mucosa	stomach
9	chr6:33574400-33583200	Enhancers	HMEC	breast
10	chr6:33574600-33580000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:33574600-33582400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:33574800-33579600	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr6:33575000-33579600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr6:33575000-33580200	Enhancers	A549	lung
15	chr6:33575200-33577400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr6:33575200-33577600	Weak transcription	Fetal Intestine Small	intestine
17	chr6:33575400-33579000	Enhancers	NHDF-Ad	bronchial
18	chr6:33575400-33579200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:33575600-33577400	Weak transcription	NHEK	skin
20	chr6:33575600-33578000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr6:33575600-33578000	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr6:33575600-33578600	Weak transcription	Esophagus	oesophagus
23	chr6:33575600-33579200	Enhancers	Fetal Lung	lung
24	chr6:33575800-33577600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr6:33575800-33578000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr6:33575800-33579000	Enhancers	Right Ventricle	heart
27	chr6:33575800-33579200	Enhancers	HSMM	muscle
28	chr6:33575800-33579400	Enhancers	Right Atrium	heart
29	chr6:33576000-33577400	Bivalent Enhancer	HepG2	liver
30	chr6:33576000-33577800	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr6:33576000-33579000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr6:33576200-33577400	Weak transcription	Primary B cells from peripheral blood	blood
33	chr6:33576200-33577600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr6:33576200-33577600	Enhancers	HSMMtube	muscle
35	chr6:33576200-33577800	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr6:33576200-33578000	Weak transcription	Gastric	stomach
37	chr6:33576200-33578800	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr6:33576200-33579600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr6:33576400-33577400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr6:33576400-33578000	Enhancers	K562	blood
41	chr6:33576400-33578600	Enhancers	Muscle Satellite Cultured Cells	--
42	chr6:33576400-33578800	Enhancers	NHLF	lung
43	chr6:33576400-33579000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
44	chr6:33576400-33579600	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr6:33576400-33579600	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr6:33576400-33579600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr6:33576400-33579600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr6:33576400-33580000	Enhancers	Left Ventricle	heart
49	chr6:33576600-33577800	Enhancers	Psoas Muscle	Psoas
50	chr6:33576600-33579000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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