Variant report

Variant	rs10877029
Chromosome Location	chr12:58256010-58256011
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: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	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:
8	chr12:58164677..58167547-chr12:58254017..58256038,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000257921	Chromatin interaction
ENSG00000123427	Chromatin interaction
ENSG00000037897	Chromatin interaction
ENSG00000245651	Chromatin interaction
ENSG00000175215	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 28 )

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

rs_ID	r²[population]
rs10431552	0.83[JPT][hapmap]
rs10444569	0.87[AMR][1000 genomes];0.86[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	0.89[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];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10747787	0.89[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];0.87[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];0.82[TSI][hapmap];0.81[AMR][1000 genomes]
rs10783851	0.84[CHD][hapmap];0.87[JPT][hapmap];0.82[TSI][hapmap];0.81[AMR][1000 genomes]
rs10783854	0.87[CEU][hapmap];0.87[JPT][hapmap];0.87[AMR][1000 genomes];0.89[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];0.89[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];0.89[TSI][hapmap]
rs10877030	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];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10877032	0.85[AMR][1000 genomes];0.83[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];0.90[EUR][1000 genomes]
rs11172362	0.89[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];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11172368	0.83[AMR][1000 genomes];0.84[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];0.85[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];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12319233	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12426201	0.87[AMR][1000 genomes];0.86[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];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1599931	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[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];0.84[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];0.87[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.86[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	0.83[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];0.98[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];0.86[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];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59401446	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6581155	0.83[JPT][hapmap]
rs703842	0.83[JPT][hapmap]
rs7134797	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs724834	0.83[JPT][hapmap]
rs7298479	0.87[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];0.86[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];0.85[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];0.86[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:28)

SNP	Gene	Cis/trans	Tissue	Source
rs10877029	MUCL1	cis	parietal	SCAN
rs10877029	CDK2	cis	parietal	SCAN
rs10877029	FAM119B	cis	lymphoblastoid	seeQTL
rs10877029	XRCC6BP1	cis	Artery Tibial	GTEx
rs10877029	STAT6	cis	cerebellum	SCAN
rs10877029	TSFM	cis	lymphoblastoid	seeQTL
rs10877029	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs10877029	METTL21B	cis	lung	GTEx
rs10877029	XRCC6BP1	cis	lung	GTEx
rs10877029	XRCC6BP1	cis	Esophagus Muscularis	GTEx
rs10877029	FAM119B	cis	Lymphoblastoid	GTEx
rs10877029	DKFZP586D0919	cis	multi-tissue	Pritchard
rs10877029	XRCC6BP1	cis	multi-tissue	Pritchard
rs10877029	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs10877029	FAM119B	cis	brain	seeQTL
rs10877029	FAM119B	cis	Frontal Cortex	GTEx
rs10877029	XRCC6BP1	cis	lymphoblastoid	seeQTL
rs10877029	XRCC6BP1	cis	brain	seeQTL
rs10877029	XRCC6BP1	cis	Whole Blood	GTEx
rs10877029	TSFM	cis	multi-tissue	Pritchard
rs10877029	FAM119B	cis	Temporal Cortex	GTEx
rs10877029	TSPAN31	cis	parietal	SCAN
rs10877029	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs10877029	FAM119B	cis	cerebellum	SCAN
rs10877029	PPP1R1A	cis	parietal	SCAN
rs10877029	LRP1	cis	parietal	SCAN
rs10877029	XRCC6BP1	cis	Artery Aorta	GTEx
rs10877029	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:34 , 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	chr12:58255400-58256200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
8	chr12:58255400-58256200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr12:58255400-58256200	Enhancers	Skeletal Muscle Female	skeletal muscle
10	chr12:58255400-58256200	Enhancers	Hela-S3	cervix
11	chr12:58255400-58256400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:58255400-58256400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr12:58255400-58256600	Enhancers	Fetal Lung	lung
14	chr12:58255400-58258800	Enhancers	HMEC	breast
15	chr12:58255600-58256200	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr12:58255600-58257000	Weak transcription	Fetal Brain Male	brain
17	chr12:58255800-58256400	Enhancers	Spleen	Spleen
18	chr12:58255800-58257400	Weak transcription	Brain Germinal Matrix	brain
19	chr12:58256000-58257000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr12:58256000-58257200	Weak transcription	NHEK	skin
21	chr12:58256000-58257400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr12:58256000-58257600	Weak transcription	Placenta	Placenta
23	chr12:58256000-58257600	Weak transcription	NH-A	brain
24	chr12:58256000-58258000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr12:58256000-58258000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr12:58256000-58258000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr12:58256000-58258000	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr12:58256000-58258000	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr12:58256000-58258000	Weak transcription	A549	lung
30	chr12:58256000-58258200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:58256000-58258200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr12:58256000-58258400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr12:58256000-58258600	Weak transcription	K562	blood
34	chr12:58256000-58259000	Weak transcription	Gastric	stomach

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