Variant report

Variant	rs200471
Chromosome Location	chr6:27763793-27763794
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27100250..27106326-chr6:27760451..27766140,11	K562	blood:
2	chr6:27740046..27740698-chr6:27763330..27763891,2	MCF-7	breast:
3	chr6:27540299..27542115-chr6:27762367..27763955,2	K562	blood:
4	chr6:27732357..27733285-chr6:27763315..27764267,2	K562	blood:
5	chr6:27100655..27103990-chr6:27762026..27765564,3	K562	blood:
6	chr6:27486715..27487216-chr6:27763770..27764509,2	K562	blood:
7	chr6:27254642..27256406-chr6:27762227..27764369,2	K562	blood:
8	chr6:27104118..27107097-chr6:27763106..27766140,3	K562	blood:
9	chr6:27155042..27157581-chr6:27762343..27765282,2	K562	blood:
10	chr6:27113828..27116369-chr6:27762956..27765394,4	MCF-7	breast:
11	chr6:27113327..27117617-chr6:27761285..27764881,4	MCF-7	breast:
12	chr6:27763793..27764319-chr6:27862939..27863691,3	K562	blood:
13	chr6:27112343..27120362-chr6:27757252..27765476,17	K562	blood:
14	chr6:27111619..27120059-chr6:27760198..27767915,14	K562	blood:
15	chr6:26572531..26573417-chr6:27763424..27764003,2	MCF-7	breast:
16	chr6:27763449..27765293-chr6:27766819..27768521,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000197903	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000265565	Chromatin interaction
ENSG00000198339	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000124635	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs11962485	1.00[CEU][hapmap]
rs11962868	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs11966528	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs11970638	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs12174918	0.91[ASN][1000 genomes]
rs175597	0.85[ASN][1000 genomes]
rs183225	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200466	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200469	0.81[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs200473	0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs200478	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs200479	0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs200481	0.89[ASN][1000 genomes]
rs200482	0.89[ASN][1000 genomes]
rs200483	0.91[ASN][1000 genomes]
rs200484	0.85[ASN][1000 genomes]
rs200485	0.89[ASN][1000 genomes]
rs200488	0.85[ASN][1000 genomes]
rs200489	0.85[ASN][1000 genomes]
rs200497	0.83[ASN][1000 genomes]
rs200498	0.81[ASN][1000 genomes]
rs200501	0.85[ASN][1000 genomes]
rs200948	0.81[ASN][1000 genomes]
rs200950	0.81[ASN][1000 genomes]
rs200952	0.81[ASN][1000 genomes]
rs200954	0.81[ASN][1000 genomes]
rs200983	0.85[ASN][1000 genomes]
rs200989	0.85[ASN][1000 genomes]
rs200990	0.83[ASN][1000 genomes]
rs200992	0.83[ASN][1000 genomes]
rs200995	0.85[ASN][1000 genomes]
rs200996	0.85[ASN][1000 genomes]
rs201002	0.83[ASN][1000 genomes]
rs2277104	0.83[ASN][1000 genomes]
rs2394001	0.91[ASN][1000 genomes]
rs2747054	0.87[ASN][1000 genomes]
rs34295134	0.85[ASN][1000 genomes]
rs36108923	0.85[ASN][1000 genomes]
rs370155	0.83[ASN][1000 genomes]
rs390764	0.87[ASN][1000 genomes]
rs401754	0.87[ASN][1000 genomes]
rs401763	0.85[ASN][1000 genomes]
rs4713122	0.91[ASN][1000 genomes]
rs4713124	0.91[ASN][1000 genomes]
rs480699	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56002038	0.87[EUR][1000 genomes]
rs56870390	0.85[ASN][1000 genomes]
rs59015666	0.91[ASN][1000 genomes]
rs59199903	0.87[EUR][1000 genomes]
rs666846	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6901437	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs6901712	0.87[EUR][1000 genomes]
rs6906980	0.81[EUR][1000 genomes]
rs6908615	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs6915101	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6922530	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs6936952	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs6938018	0.87[EUR][1000 genomes]
rs9348779	0.81[ASN][1000 genomes]
rs9368531	0.87[ASN][1000 genomes]
rs9368534	0.83[ASN][1000 genomes]
rs9368535	0.81[ASN][1000 genomes]
rs9368536	0.81[ASN][1000 genomes]
rs9380018	0.89[ASN][1000 genomes]
rs9393858	0.87[ASN][1000 genomes]
rs9461422	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs9468227	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs9468262	1.00[CEU][hapmap];1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv830618	chr6:27593274-27789605	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	143 gene(s)	inside rSNPs	diseases
3	nsv432858	chr6:27719375-28011652	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	387 gene(s)	inside rSNPs	diseases
4	nsv1017440	chr6:27734824-27864277	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	370 gene(s)	inside rSNPs	diseases
5	nsv1022173	chr6:27734824-27959408	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
6	nsv1017057	chr6:27745777-27789683	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	125 gene(s)	inside rSNPs	diseases
7	nsv883512	chr6:27748631-27969004	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs200471	Hs.158943	cis	multi-tissue	Pritchard

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27760600-27763800	Weak transcription	Colon Smooth Muscle	Colon
2	chr6:27760800-27764000	Weak transcription	Lung	lung
3	chr6:27761200-27763800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:27761200-27763800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr6:27761200-27763800	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr6:27761200-27763800	Weak transcription	Primary B cells from peripheral blood	blood
7	chr6:27761200-27763800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr6:27761200-27763800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr6:27761200-27764000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr6:27761200-27764000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr6:27761200-27764000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr6:27761200-27764000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr6:27761200-27764000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:27761200-27764000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:27761200-27764200	Enhancers	Fetal Intestine Large	intestine
16	chr6:27761200-27765000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr6:27761200-27768600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr6:27761400-27763800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr6:27761400-27763800	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr6:27761400-27763800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr6:27761600-27763800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr6:27761600-27764000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:27761600-27768600	Weak transcription	NHEK	skin
24	chr6:27761800-27764200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr6:27762000-27764200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr6:27762000-27764200	Weak transcription	Brain Germinal Matrix	brain
27	chr6:27762800-27764000	Enhancers	Hela-S3	cervix
28	chr6:27763000-27763800	Enhancers	Dnd41	blood
29	chr6:27763200-27764400	Enhancers	GM12878-XiMat	blood
30	chr6:27763400-27763800	Enhancers	HepG2	liver
31	chr6:27763400-27764000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:27763400-27764600	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr6:27763400-27765600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr6:27763600-27763800	Enhancers	Thymus	Thymus
35	chr6:27763600-27763800	Enhancers	K562	blood
36	chr6:27763600-27764200	Weak transcription	Fetal Lung	lung

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