Variant report

Variant	rs566742
Chromosome Location	chr6:36395668-36395669
allele	A/G
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:36391946..36393446-chr6:36395564..36398109,2	MCF-7	breast:
2	chr6:36388375..36397373-chr6:36559893..36568556,25	K562	blood:
3	chr6:36389566..36392929-chr6:36393759..36397072,6	K562	blood:
4	chr6:36388047..36404187-chr6:36407090..36418492,47	K562	blood:
5	chr6:36393812..36400727-chr6:36401208..36405433,7	K562	blood:
6	chr6:36389876..36393968-chr6:36394401..36398329,5	MCF-7	breast:
7	chr6:36395657..36401114-chr6:36407932..36413764,7	MCF-7	breast:
8	chr6:36388539..36397962-chr6:36560062..36566089,23	K562	blood:

No data

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

Extended variants
information (count: 74 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:73)

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];0.82[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];0.93[AFR][1000 genomes];0.98[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]
rs12209346	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12214285	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12215889	0.98[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	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1744654	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2187810	0.80[CHD][hapmap]
rs3752478	0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap];0.83[ASN][1000 genomes]
rs3798471	0.83[ASN][1000 genomes]
rs4140593	0.91[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap];0.87[ASN][1000 genomes]
rs4711450	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];0.95[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs515129	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs515186	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs517890	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs522179	0.88[AFR][1000 genomes];1.00[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];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs546272	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs546353	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs547026	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs547966	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57389119	0.88[ASN][1000 genomes]
rs584196	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs584418	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59440875	0.91[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];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs597153	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs600192	0.99[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];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs609067	0.81[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];0.84[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];0.84[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];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs628213	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs628314	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs629297	0.88[AFR][1000 genomes];1.00[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];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs629721	0.92[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];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6457918	0.86[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];0.84[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];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs668499	0.95[CEU][hapmap];0.81[CHB][hapmap]
rs6906885	0.82[CHD][hapmap]
rs6919571	0.82[ASW][hapmap];0.83[CHD][hapmap];0.94[LWK][hapmap];0.92[MKK][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes]
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];0.84[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];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs853873	0.80[ASN][1000 genomes]
rs853881	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs853882	0.84[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	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9296180	0.83[CHD][hapmap];0.94[LWK][hapmap];0.92[MKK][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes]
rs9296181	0.83[YRI][hapmap];0.81[AFR][1000 genomes]
rs9357212	0.81[AFR][1000 genomes]
rs9357214	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9368930	0.81[AFR][1000 genomes]
rs9368931	0.83[YRI][hapmap];0.82[AFR][1000 genomes]
rs9380569	0.82[AFR][1000 genomes]
rs9380572	0.82[AFR][1000 genomes]
rs9394349	0.83[YRI][hapmap];0.82[AFR][1000 genomes]
rs9470270	0.83[YRI][hapmap]
rs9470274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9470278	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]
rs9470285	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9470309	0.81[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
rs566742	HMGA1	cis	parietal	SCAN
rs566742	TULP1	cis	cerebellum	SCAN
rs566742	ETV7	cis	Whole Blood	GTEx
rs566742	RPL10A	cis	cerebellum	SCAN
rs566742	C6orf1	cis	parietal	SCAN
rs566742	PNPLA1	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36391800-36397600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:36392000-36398800	Weak transcription	Osteobl	bone
3	chr6:36392000-36399200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:36392000-36400000	Weak transcription	Fetal Heart	heart
5	chr6:36392000-36404200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr6:36392400-36396800	Weak transcription	Placenta	Placenta
7	chr6:36393800-36399600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:36394200-36399600	Weak transcription	NHEK	skin
9	chr6:36394200-36399800	Weak transcription	HMEC	breast
10	chr6:36395200-36396000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr6:36395400-36396000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:36395400-36396000	Enhancers	HSMM	muscle
13	chr6:36395600-36395800	Enhancers	HepG2	liver
14	chr6:36395600-36396000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr6:36395600-36396000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr6:36395600-36396000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr6:36395600-36396000	Enhancers	A549	lung
18	chr6:36395600-36396000	Flanking Active TSS	Hela-S3	cervix
19	chr6:36395600-36396000	Enhancers	HSMMtube	muscle
20	chr6:36395600-36396400	Flanking Active TSS	K562	blood

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