Variant report

Variant	rs9470278
Chromosome Location	chr6:36399239-36399240
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:36388047..36404187-chr6:36407090..36418492,47	K562	blood:
2	chr6:36393812..36400727-chr6:36401208..36405433,7	K562	blood:
3	chr6:36390037..36391654-chr6:36397187..36400029,2	K562	blood:
4	chr6:36395657..36401114-chr6:36407932..36413764,7	MCF-7	breast:
5	chr6:36397591..36399508-chr6:36561399..36563224,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112081	Chromatin interaction
ENSG00000179165	Chromatin interaction
ENSG00000112078	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1003250	0.83[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10440841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1076929	0.82[CHD][hapmap]
rs10947609	0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs11757823	0.82[CHD][hapmap]
rs12209346	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12214285	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12215889	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1570368	0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs1742757	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1744654	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2187810	0.82[CHD][hapmap]
rs2234071	0.81[CHD][hapmap]
rs3752478	0.95[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap];0.83[ASN][1000 genomes]
rs3798471	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4140593	0.91[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap];0.87[ASN][1000 genomes]
rs4711450	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4711452	0.95[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs4711453	0.95[CHB][hapmap];0.98[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs515129	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs515186	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs517890	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs522179	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs544267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs546272	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs546353	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs547026	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs547966	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs566742	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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57389119	0.88[ASN][1000 genomes]
rs584196	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs584418	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59440875	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs595954	0.83[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs597153	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs600192	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs605684	0.91[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs609067	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs614028	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs619011	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs621796	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs628213	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs628314	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs629297	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs629560	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs629721	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs632943	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6457918	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs648125	0.84[CEU][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs659726	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs664370	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs668499	0.95[CEU][hapmap];0.81[CHB][hapmap]
rs6906885	0.84[CHD][hapmap]
rs6919571	0.82[ASW][hapmap];0.85[CHD][hapmap];0.94[LWK][hapmap];0.92[MKK][hapmap];0.83[YRI][hapmap]
rs6923993	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73411054	0.88[ASN][1000 genomes]
rs7744363	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs853873	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs853881	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs853882	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs860513	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs863815	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9296180	0.85[CHD][hapmap];0.94[LWK][hapmap];0.92[MKK][hapmap];0.83[YRI][hapmap]
rs9296181	0.83[YRI][hapmap]
rs9357214	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9368931	0.83[YRI][hapmap]
rs9394349	0.83[YRI][hapmap]
rs9470270	0.83[YRI][hapmap]
rs9470274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9470285	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9470309	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[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	nsv885806	chr6:36349890-36621178	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9470278	RPL10A	cis	cerebellum	SCAN
rs9470278	HMGA1	cis	parietal	SCAN
rs9470278	ETV7	cis	Whole Blood	GTEx
rs9470278	C6orf1	cis	parietal	SCAN
rs9470278	TULP1	cis	cerebellum	SCAN
rs9470278	PNPLA1	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36392000-36400000	Weak transcription	Fetal Heart	heart
2	chr6:36392000-36404200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr6:36393800-36399600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr6:36394200-36399600	Weak transcription	NHEK	skin
5	chr6:36394200-36399800	Weak transcription	HMEC	breast
6	chr6:36396000-36399400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:36396000-36399400	Weak transcription	HSMM	muscle
8	chr6:36396000-36399600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:36396000-36399800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr6:36396000-36400000	Weak transcription	A549	lung
11	chr6:36397800-36400400	Enhancers	Placenta	Placenta
12	chr6:36398000-36399600	Enhancers	HepG2	liver
13	chr6:36398200-36400200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr6:36398400-36400600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr6:36398600-36399800	Weak transcription	HSMMtube	muscle
16	chr6:36398600-36400400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr6:36398800-36400800	Enhancers	Osteobl	bone
18	chr6:36399000-36399800	Enhancers	GM12878-XiMat	blood
19	chr6:36399000-36400000	Enhancers	Hela-S3	cervix
20	chr6:36399000-36400600	Enhancers	Placenta Amnion	Placenta Amnion
21	chr6:36399000-36410200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr6:36399200-36399400	Enhancers	NH-A	brain
23	chr6:36399200-36400200	Enhancers	Muscle Satellite Cultured Cells	--
24	chr6:36399200-36400400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr6:36399200-36400800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr6:36399200-36400800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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