Variant report

Variant	rs472990
Chromosome Location	chr6:33556306-33556307
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:33555689..33557372-chr6:33575674..33577429,2	MCF-7	breast:
2	chr6:33555453..33558278-chr6:33607870..33609566,2	K562	blood:
3	chr6:33556084..33559190-chr6:33561463..33564085,3	K562	blood:
4	chr6:33555432..33562879-chr6:33670455..33680174,12	K562	blood:
5	chr6:33554633..33558061-chr6:33675915..33678804,3	MCF-7	breast:
6	chr6:33553773..33556336-chr6:33668184..33671160,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137288	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1536042	1.00[ASN][1000 genomes]
rs16869178	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1705000	1.00[ASN][1000 genomes]
rs1755041	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1755042	1.00[ASN][1000 genomes]
rs1755054	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1794686	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1794688	0.87[EUR][1000 genomes];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]
rs4713647	1.00[ASN][1000 genomes]
rs4713652	1.00[ASN][1000 genomes]
rs480568	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs485623	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs535584	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs542056	1.00[ASN][1000 genomes]
rs542725	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs549719	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55700437	1.00[ASN][1000 genomes]
rs557559	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs560218	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs561276	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs572824	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59572422	1.00[ASN][1000 genomes]
rs61687548	1.00[ASN][1000 genomes]
rs6900438	1.00[ASN][1000 genomes]
rs6906810	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6928341	1.00[ASN][1000 genomes]
rs71536195	1.00[EUR][1000 genomes];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[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7775313	1.00[ASN][1000 genomes]
rs806604	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs806605	0.89[EUR][1000 genomes]
rs9368770	1.00[ASN][1000 genomes]
rs9689326	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33548400-33557000	Weak transcription	HSMM	muscle
2	chr6:33548400-33557200	Weak transcription	NHDF-Ad	bronchial
3	chr6:33548400-33557600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:33548400-33557800	Weak transcription	Right Atrium	heart
5	chr6:33548600-33560600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr6:33548800-33557800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr6:33551800-33557200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:33552000-33557000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr6:33553600-33557000	Weak transcription	Ovary	ovary
10	chr6:33553600-33558000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr6:33553800-33556400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr6:33553800-33556400	Weak transcription	Fetal Intestine Small	intestine
13	chr6:33553800-33556600	Weak transcription	Fetal Intestine Large	intestine
14	chr6:33553800-33556600	Weak transcription	Lung	lung
15	chr6:33553800-33556600	Weak transcription	Pancreas	Pancrea
16	chr6:33553800-33556800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr6:33553800-33556800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr6:33553800-33556800	Weak transcription	Stomach Mucosa	stomach
19	chr6:33553800-33557000	Weak transcription	Fetal Stomach	stomach
20	chr6:33553800-33557000	Weak transcription	HMEC	breast
21	chr6:33553800-33557000	Weak transcription	HSMMtube	muscle
22	chr6:33553800-33557200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr6:33553800-33557200	Weak transcription	Fetal Heart	heart
24	chr6:33553800-33557400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr6:33553800-33557400	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr6:33553800-33557600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:33553800-33557600	Weak transcription	Left Ventricle	heart
28	chr6:33553800-33557600	Weak transcription	NH-A	brain
29	chr6:33553800-33557600	Weak transcription	Osteobl	bone
30	chr6:33553800-33557800	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr6:33553800-33557800	Weak transcription	Esophagus	oesophagus
32	chr6:33553800-33558400	Weak transcription	Gastric	stomach
33	chr6:33553800-33560400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr6:33554000-33556400	Weak transcription	Right Ventricle	heart
35	chr6:33554000-33556600	Weak transcription	Colonic Mucosa	Colon
36	chr6:33554000-33556600	Weak transcription	Hela-S3	cervix
37	chr6:33554000-33556600	Weak transcription	HUVEC	blood vessel
38	chr6:33554000-33557000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr6:33554000-33557000	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr6:33554000-33557000	Weak transcription	Adipose Nuclei	Adipose
41	chr6:33554000-33557000	Weak transcription	Fetal Lung	lung
42	chr6:33554000-33557200	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr6:33554000-33557200	Weak transcription	Placenta	Placenta
44	chr6:33554000-33557200	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr6:33554000-33557400	Weak transcription	Colon Smooth Muscle	Colon
46	chr6:33554000-33557600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr6:33554000-33557600	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr6:33554000-33557600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr6:33554000-33557600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr6:33554000-33557600	Weak transcription	Brain Cingulate Gyrus	brain

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