Variant report

Variant	rs10877030
Chromosome Location	chr12:58256714-58256715
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:58247895..58249624-chr12:58254924..58257360,2	K562	blood:
2	chr12:58248124..58250440-chr12:58255143..58257360,2	K562	blood:
3	chr12:58254046..58258722-chr12:58273553..58277019,6	MCF-7	breast:
4	chr12:58254019..58259551-chr12:58280629..58287945,9	MCF-7	breast:
5	chr12:58255940..58258991-chr12:58263646..58265441,3	K562	blood:
6	chr12:58237213..58243657-chr12:58255578..58259317,18	MCF-7	breast:
7	chr12:58255415..58256919-chr12:58282201..58284913,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000245651	Chromatin interaction
ENSG00000175215	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 25 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10431552	0.83[JPT][hapmap]
rs10444569	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10747783	0.83[JPT][hapmap]
rs10747784	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10747786	0.94[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10747787	0.94[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10783847	0.83[JPT][hapmap]
rs10783848	0.80[JPT][hapmap]
rs10783850	0.80[CHD][hapmap];0.87[JPT][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes]
rs10783851	0.84[CHD][hapmap];0.87[JPT][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes]
rs10783854	0.87[CEU][hapmap];0.87[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10783855	0.88[CEU][hapmap];0.87[CHD][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10783856	0.91[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10877012	0.83[JPT][hapmap]
rs10877014	0.83[JPT][hapmap]
rs10877015	0.83[JPT][hapmap]
rs10877016	0.83[JPT][hapmap]
rs10877019	0.83[JPT][hapmap]
rs10877022	0.81[AMR][1000 genomes]
rs10877024	0.81[AMR][1000 genomes]
rs10877025	0.81[AMR][1000 genomes]
rs10877026	0.82[AMR][1000 genomes]
rs10877028	0.88[CEU][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap]
rs10877029	0.94[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877031	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10877032	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11172333	0.83[JPT][hapmap]
rs11172335	0.83[JPT][hapmap]
rs11172343	0.83[JPT][hapmap]
rs11172344	0.83[JPT][hapmap]
rs11172349	0.83[JPT][hapmap]
rs11172351	0.83[JPT][hapmap]
rs11172361	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11172362	0.88[EUR][1000 genomes]
rs11172367	0.88[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11172368	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11172369	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11172371	0.82[CHB][hapmap];0.80[ASN][1000 genomes]
rs11172378	0.82[CHB][hapmap];0.90[CHD][hapmap]
rs12312955	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12319233	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12426201	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1599750	0.88[CEU][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1599751	0.88[CEU][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1599931	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1875124	0.83[JPT][hapmap]
rs1875125	0.94[JPT][hapmap];0.80[AMR][1000 genomes]
rs1962047	0.82[CHB][hapmap];0.93[CHD][hapmap]
rs2002275	0.84[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3825079	0.83[JPT][hapmap]
rs4237844	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4237845	0.93[CHD][hapmap]
rs4630335	0.84[CHD][hapmap]
rs4646536	0.83[JPT][hapmap]
rs4760171	0.91[GIH][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap];0.82[AMR][1000 genomes]
rs4760172	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4760332	0.94[JPT][hapmap]
rs4760333	0.83[AMR][1000 genomes]
rs4760335	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4760339	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4760340	0.87[CHB][hapmap];0.97[CHD][hapmap]
rs4760341	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs5017863	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59401446	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6581155	0.83[JPT][hapmap]
rs703842	0.83[JPT][hapmap]
rs7134797	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs724834	0.83[JPT][hapmap]
rs7298479	0.85[EUR][1000 genomes]
rs7312623	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7489290	0.92[JPT][hapmap];0.85[AMR][1000 genomes]
rs7954957	0.93[CHD][hapmap]
rs7969844	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7971877	0.83[CHD][hapmap]
rs8181644	0.83[JPT][hapmap]
rs870392	0.83[CHD][hapmap];0.94[JPT][hapmap]
rs871871	0.83[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap]
rs923829	0.83[JPT][hapmap]
rs9645819	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[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	nsv559046	chr12:58162085-58478598	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	261 gene(s)	inside rSNPs	diseases

mRNA abundance (count:25)

SNP	Gene	Cis/trans	Tissue	Source
rs10877030	XRCC6BP1	cis	lung	GTEx
rs10877030	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs10877030	TSFM	cis	lymphoblastoid	seeQTL
rs10877030	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs10877030	XRCC6BP1	cis	lymphoblastoid	seeQTL
rs10877030	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs10877030	XRCC6BP1	cis	Artery Aorta	GTEx
rs10877030	FAM119B	cis	Frontal Cortex	GTEx
rs10877030	MUCL1	cis	parietal	SCAN
rs10877030	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs10877030	FAM119B	cis	Temporal Cortex	GTEx
rs10877030	METTL21B	cis	lung	GTEx
rs10877030	XRCC6BP1	cis	Esophagus Muscularis	GTEx
rs10877030	STAT6	cis	cerebellum	SCAN
rs10877030	FAM119B	cis	Lymphoblastoid	GTEx
rs10877030	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs10877030	XRCC6BP1	cis	Artery Tibial	GTEx
rs10877030	XRCC6BP1	cis	Whole Blood	GTEx
rs10877030	FAM119B	cis	cerebellum	SCAN
rs10877030	CDK2	cis	parietal	SCAN
rs10877030	TSPAN31	cis	parietal	SCAN
rs10877030	LRP1	cis	parietal	SCAN
rs10877030	FAM119B	cis	lymphoblastoid	seeQTL
rs10877030	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs10877030	PPP1R1A	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58247800-58257400	Weak transcription	Right Ventricle	heart
2	chr12:58248800-58257200	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr12:58249200-58257800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr12:58250400-58257800	Weak transcription	Fetal Intestine Small	intestine
5	chr12:58254200-58257600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr12:58254400-58258400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:58255400-58258800	Enhancers	HMEC	breast
8	chr12:58255600-58257000	Weak transcription	Fetal Brain Male	brain
9	chr12:58255800-58257400	Weak transcription	Brain Germinal Matrix	brain
10	chr12:58256000-58257000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr12:58256000-58257200	Weak transcription	NHEK	skin
12	chr12:58256000-58257400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr12:58256000-58257600	Weak transcription	Placenta	Placenta
14	chr12:58256000-58257600	Weak transcription	NH-A	brain
15	chr12:58256000-58258000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr12:58256000-58258000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr12:58256000-58258000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr12:58256000-58258000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr12:58256000-58258000	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr12:58256000-58258000	Weak transcription	A549	lung
21	chr12:58256000-58258200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:58256000-58258200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr12:58256000-58258400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr12:58256000-58258600	Weak transcription	K562	blood
25	chr12:58256000-58259000	Weak transcription	Gastric	stomach
26	chr12:58256200-58256800	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr12:58256200-58257200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr12:58256200-58257800	Weak transcription	Hela-S3	cervix
29	chr12:58256400-58256800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr12:58256400-58258000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr12:58256400-58264600	Weak transcription	Spleen	Spleen
32	chr12:58256600-58257000	Weak transcription	Fetal Lung	lung
33	chr12:58256600-58258400	Enhancers	HSMM	muscle

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