Variant report

Variant	rs1028308
Chromosome Location	chr6:27129757-27129758
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:19)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:19 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:27129016..27131060-chr6:27203219..27204957,2	K562	blood:
2	chr6:27128393..27129996-chr6:27862563..27865098,2	MCF-7	breast:
3	chr6:27129652..27132851-chr6:27133864..27136225,4	MCF-7	breast:
4	chr6:27129504..27130005-chr6:27760938..27761839,2	K562	blood:
5	chr6:27124141..27131442-chr6:27773840..27780959,15	K562	blood:
6	chr6:27129261..27130116-chr6:27719696..27720311,2	MCF-7	breast:
7	chr6:27127283..27131812-chr6:27144311..27148515,7	MCF-7	breast:
8	chr6:27127689..27130005-chr6:27798100..27799751,2	MCF-7	breast:
9	chr6:27128425..27130087-chr6:27629956..27632184,2	MCF-7	breast:
10	chr6:27128837..27130476-chr6:28186334..28188871,2	K562	blood:
11	chr6:27129334..27133279-chr6:27777254..27779059,3	MCF-7	breast:
12	chr6:27129411..27129971-chr6:27759594..27760127,2	MCF-7	breast:
13	chr6:27129337..27130597-chr6:27759299..27760721,7	K562	blood:
14	chr6:27128299..27130552-chr6:27519554..27521121,2	K562	blood:
15	chr6:27124460..27128154-chr6:27128397..27131899,6	MCF-7	breast:
16	chr6:27128785..27131507-chr6:27205478..27207504,2	K562	blood:
17	chr6:27128242..27130382-chr6:27772213..27774581,2	K562	blood:
18	chr6:27128038..27130307-chr6:27858390..27861349,2	MCF-7	breast:
19	chr6:27128785..27131349-chr6:27205137..27206978,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000185130	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000217862	Chromatin interaction
ENSG00000203813	Chromatin interaction
ENSG00000197914	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000196747	Chromatin interaction
ENSG00000196331	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10946899	0.83[CEU][hapmap]
rs11756275	0.84[JPT][hapmap]
rs12527111	0.84[JPT][hapmap]
rs2022272	0.96[CEU][hapmap];0.89[CHB][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.88[EUR][1000 genomes]
rs2142685	0.84[JPT][hapmap]
rs2393915	0.84[JPT][hapmap]
rs2393918	0.80[JPT][hapmap]
rs4582379	0.80[JPT][hapmap]
rs4713069	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs6456766	0.85[EUR][1000 genomes]
rs6456767	0.84[JPT][hapmap]
rs6456768	0.84[JPT][hapmap]
rs6921388	0.88[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6925226	0.88[EUR][1000 genomes]
rs6930508	0.84[JPT][hapmap]
rs7744759	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7745603	0.80[TSI][hapmap]
rs7747454	0.84[JPT][hapmap]
rs7764984	0.84[EUR][1000 genomes]
rs858964	0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9295730	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[TSI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9348750	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9348751	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9379960	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9393790	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9393791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9461335	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs994691	0.84[JPT][hapmap]

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	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1028308	HIST1H2BM	cis	cerebellum	SCAN
rs1028308	BTN2A1	cis	parietal	SCAN
rs1028308	BTN3A2	cis	lymphoblastoid	seeQTL
rs1028308	BTN3A3	cis	parietal	SCAN
rs1028308	BTN3A2	Cis_1M	lymphoblastoid	RTeQTL
rs1028308	BTN3A2	cis	cerebellum	SCAN
rs1028308	ZKSCAN3	cis	parietal	SCAN
rs1028308	HIST1H2BH	cis	cerebellum	SCAN
rs1028308	BTN3A3	cis	cerebellum	SCAN
rs1028308	Hs.158943	cis	multi-tissue	Pritchard

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27126000-27135800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:27126200-27131200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr6:27126200-27136000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:27126400-27131400	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr6:27128400-27129800	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr6:27129000-27129800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr6:27129200-27129800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr6:27129200-27129800	Enhancers	Dnd41	blood
9	chr6:27129200-27129800	Enhancers	NHEK	skin
10	chr6:27129200-27130000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr6:27129400-27130000	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr6:27129400-27130000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr6:27129400-27132400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr6:27129600-27129800	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr6:27129600-27130000	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr6:27129600-27130000	Active TSS	HUES6 Cell Line	embryonic stem cell
17	chr6:27129600-27130400	Active TSS	K562	blood
18	chr6:27129600-27130600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr6:27129600-27130600	Enhancers	A549	lung

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