Variant report

Variant	rs2799076
Chromosome Location	chr6:28232278-28232279
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:28231755-28232754	K562	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28108136..28111844-chr6:28229127..28232755,4	K562	blood:
2	chr6:28020207..28021946-chr6:28231611..28234328,2	K562	blood:
3	chr6:28196925..28198715-chr6:28230690..28232627,2	K562	blood:
4	chr6:28232169..28234255-chr6:28237329..28239836,2	MCF-7	breast:
5	chr6:28192920..28194978-chr6:28231042..28233452,2	K562	blood:
6	chr6:28184789..28191313-chr6:28230652..28235913,7	K562	blood:
7	chr6:28230426..28232674-chr6:28234865..28236670,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000197062	TF binding region
ENSG00000198315	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000137185	Chromatin interaction
ENSG00000182477	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10080420	0.83[ASN][1000 genomes]
rs10484404	1.00[JPT][hapmap]
rs1150700	0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap]
rs1150715	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1150722	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1150723	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1150725	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1225600	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1225604	0.88[YRI][hapmap]
rs12332986	0.83[ASN][1000 genomes]
rs1233709	0.88[YRI][hapmap]
rs1600621	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1679705	0.88[YRI][hapmap]
rs1679723	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[ASN][1000 genomes]
rs1736889	0.88[YRI][hapmap]
rs1736892	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[ASN][1000 genomes]
rs1778510	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2108924	1.00[GIH][hapmap];1.00[JPT][hapmap]
rs2191036	0.83[ASN][1000 genomes]
rs28475822	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2859375	1.00[JPT][hapmap]
rs3757180	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3757183	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs6456812	0.86[ASW][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[ASN][1000 genomes]
rs6456817	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6456820	0.83[ASN][1000 genomes]
rs6899512	0.83[ASN][1000 genomes]
rs6901001	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[ASN][1000 genomes]
rs6902583	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6908459	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[ASN][1000 genomes]
rs6910120	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[ASN][1000 genomes]
rs6912921	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6918023	1.00[YRI][hapmap]
rs6918043	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[ASN][1000 genomes]
rs6918631	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[ASN][1000 genomes]
rs6922161	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6922302	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6927023	0.83[ASN][1000 genomes]
rs6929449	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[ASN][1000 genomes]
rs6929559	1.00[JPT][hapmap]
rs6938371	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6941222	0.83[ASN][1000 genomes]
rs7747772	1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7752448	1.00[JPT][hapmap]
rs7752721	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs7759855	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7767897	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9295769	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[ASN][1000 genomes]
rs9295770	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9461450	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9461452	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9461453	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9461457	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9468328	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9468335	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9468337	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9468341	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9468363	1.00[YRI][hapmap]
rs9468369	1.00[YRI][hapmap]
rs9468375	0.90[ASN][1000 genomes]
rs9468384	0.83[ASN][1000 genomes]
rs9654587	0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28227000-28233800	Weak transcription	Primary T helper cells PMA-I stimulated	--
2	chr6:28227400-28234400	Weak transcription	HSMMtube	muscle
3	chr6:28227600-28233600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:28227600-28233800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr6:28227600-28233800	Weak transcription	HMEC	breast
6	chr6:28227800-28234400	Weak transcription	Right Atrium	heart
7	chr6:28228200-28234600	Weak transcription	Left Ventricle	heart
8	chr6:28228400-28233800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr6:28228400-28234000	Weak transcription	Psoas Muscle	Psoas
10	chr6:28230000-28233800	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr6:28230000-28234200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr6:28230400-28234600	Weak transcription	Right Ventricle	heart
13	chr6:28231400-28233200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr6:28231600-28232400	Enhancers	Muscle Satellite Cultured Cells	--
15	chr6:28231600-28232400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr6:28231800-28233400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr6:28232000-28233800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr6:28232000-28233800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr6:28232000-28233800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr6:28232000-28234400	Enhancers	Hela-S3	cervix
21	chr6:28232200-28232400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr6:28232200-28232400	Bivalent Enhancer	HUVEC	blood vessel
23	chr6:28232200-28233800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr6:28232200-28234000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr6:28232200-28234000	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr6:28232200-28234200	Weak transcription	Primary T cells from cord blood	blood
27	chr6:28232200-28234200	Weak transcription	Osteobl	bone

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