Variant report

Variant	rs946631
Chromosome Location	chr1:180525064-180525065
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr1:180523473-180525316	MCF-7	breast:	n/a	n/a
2	GATA3	chr1:180524407-180525114	MCF-7	breast:	n/a	n/a
3	SIN3AK20	chr1:180524286-180525215	MCF-7	breast:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:180508398..180510494-chr1:180524364..180527463,3	K562	blood:
2	chr1:180523368..180525230-chr1:180988182..180990982,2	K562	blood:
3	chr1:180523371..180525689-chr1:180527649..180530841,3	MCF-7	breast:
4	chr1:180524735..180527713-chr1:180532458..180534651,2	K562	blood:
5	chr1:180524921..180527683-chr1:180532658..180534394,2	MCF-7	breast:
6	chr1:180523564..180525363-chr1:180582758..180585501,2	K562	blood:
7	chr1:180519806..180522795-chr1:180523226..180525284,2	MCF-7	breast:
8	chr1:180521347..180523149-chr1:180523872..180526102,2	K562	blood:
9	chr1:180523341..180525104-chr1:180600909..180602424,2	MCF-7	breast:
10	chr1:180520741..180525768-chr1:180529838..180532812,4	MCF-7	breast:
11	chr1:180523696..180527243-chr1:180568963..180571816,3	MCF-7	breast:
12	chr1:180518736..180521138-chr1:180521840..180525224,3	K562	blood:

No data

Variant related genes	Relation type
OVAAL	TF binding region
ENSG00000143324	Chromatin interaction
ENSG00000236719	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10798774	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10914021	0.81[CEU][hapmap]
rs10914022	0.81[CEU][hapmap]
rs10914023	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs10914028	0.88[ASN][1000 genomes]
rs10914034	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10914036	0.85[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.94[TSI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10914037	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12024201	0.80[CHB][hapmap]
rs12039331	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs12069581	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12407684	0.81[CEU][hapmap]
rs13374665	0.81[CEU][hapmap]
rs1416822	0.81[CEU][hapmap]
rs1538622	0.90[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs16856127	0.85[CEU][hapmap]
rs17300579	0.81[CEU][hapmap]
rs17300600	0.83[CEU][hapmap]
rs4405110	0.81[CEU][hapmap]
rs4651068	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4651069	0.84[EUR][1000 genomes]
rs6425644	0.81[CHB][hapmap]
rs6425646	0.81[CEU][hapmap]
rs6680202	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6692401	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6694798	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6694975	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6695171	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6695263	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6699076	0.87[CHB][hapmap]
rs6703124	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72720946	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72720947	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7513944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.89[TSI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7513963	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7515243	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7517775	0.81[CEU][hapmap]
rs7517902	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7540276	0.81[CHB][hapmap]
rs7541993	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7543366	0.81[CHB][hapmap]
rs7546119	0.85[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7550897	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7551178	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7552084	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs946636	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
2	nsv949311	chr1:180438895-180692815	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv872578	chr1:180510771-180842344	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs946631	RGS8	cis	cerebellum	SCAN
rs946631	ACBD6	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180510400-180529400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:180516600-180536800	Weak transcription	Psoas Muscle	Psoas
3	chr1:180521400-180525400	Weak transcription	Left Ventricle	heart
4	chr1:180521800-180530200	Weak transcription	Right Atrium	heart
5	chr1:180523200-180525200	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr1:180523200-180525600	Enhancers	Placenta	Placenta
7	chr1:180525000-180529000	Weak transcription	K562	blood

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