Variant report

Variant	rs10747787
Chromosome Location	chr12:58260657-58260658
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:58258786..58263861-chr12:58273729..58277386,6	MCF-7	breast:
2	chr12:58259629..58265686-chr12:58266089..58272179,8	K562	blood:
3	chr12:58234242..58236619-chr12:58259394..58262193,2	MCF-7	breast:
4	chr12:58257740..58261779-chr12:58273700..58278459,4	MCF-7	breast:
5	chr12:58259698..58262580-chr5:154319260..154321205,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000082515	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10431552	0.83[JPT][hapmap]
rs10444569	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10747783	0.83[JPT][hapmap]
rs10747784	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10747786	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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10783847	0.83[JPT][hapmap]
rs10783848	0.80[JPT][hapmap]
rs10783850	0.80[CHD][hapmap];0.87[JPT][hapmap]
rs10783851	0.84[CHD][hapmap];0.87[JPT][hapmap]
rs10783854	0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10783855	0.87[CHD][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10783856	0.82[AMR][1000 genomes];0.80[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]
rs10877028	0.87[CHD][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs10877029	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]
rs10877030	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]
rs10877031	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10877032	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[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	0.81[AMR][1000 genomes]
rs11172367	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11172368	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11172369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172371	0.82[CHB][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11172378	0.82[CHB][hapmap];0.90[CHD][hapmap]
rs12312955	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12319233	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12426201	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1599750	0.87[CHD][hapmap];0.86[GIH][hapmap];0.86[AMR][1000 genomes]
rs1599751	0.83[CHD][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes]
rs1599931	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1875124	0.83[JPT][hapmap]
rs1875125	0.94[JPT][hapmap]
rs1962047	0.82[CHB][hapmap];0.93[CHD][hapmap];0.80[ASN][1000 genomes]
rs2002275	0.96[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3751331	0.80[ASN][1000 genomes]
rs3825079	0.83[JPT][hapmap]
rs4237844	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4237845	0.93[CHD][hapmap]
rs4630335	0.84[CHD][hapmap]
rs4646536	0.83[JPT][hapmap]
rs4760171	0.84[GIH][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap]
rs4760172	0.83[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4760332	0.94[JPT][hapmap]
rs4760335	0.80[AMR][1000 genomes]
rs4760339	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4760340	0.87[CHB][hapmap];0.97[CHD][hapmap];0.80[ASN][1000 genomes]
rs4760341	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs5017863	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59401446	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581155	0.83[JPT][hapmap]
rs6581157	0.81[ASN][1000 genomes]
rs703842	0.83[JPT][hapmap]
rs7134797	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs724834	0.83[JPT][hapmap]
rs7312623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7489290	0.92[JPT][hapmap];0.80[AMR][1000 genomes]
rs7954957	0.93[CHD][hapmap]
rs7969844	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[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];0.84[GIH][hapmap];0.94[JPT][hapmap]
rs923829	0.83[JPT][hapmap]
rs9645819	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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:21)

SNP	Gene	Cis/trans	Tissue	Source
rs10747787	METTL21B	cis	lung	GTEx
rs10747787	XRCC6BP1	cis	lymphoblastoid	seeQTL
rs10747787	FAM119B	cis	Lymphoblastoid	GTEx
rs10747787	FAM119B	cis	brain	seeQTL
rs10747787	XRCC6BP1	cis	brain	seeQTL
rs10747787	METTL21B	cis	Adipose Subcutaneous	GTEx
rs10747787	XRCC6BP1	cis	Whole Blood	GTEx
rs10747787	FAM119B	cis	lymphoblastoid	seeQTL
rs10747787	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs10747787	XRCC6BP1	cis	Artery Tibial	GTEx
rs10747787	XRCC6BP1	cis	multi-tissue	Pritchard
rs10747787	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs10747787	XRCC6BP1	cis	lung	GTEx
rs10747787	TSFM	cis	lymphoblastoid	seeQTL
rs10747787	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs10747787	CDK2	cis	parietal	SCAN
rs10747787	TSFM	cis	parietal	SCAN
rs10747787	DKFZP586D0919	cis	multi-tissue	Pritchard
rs10747787	FAM119B	cis	cerebellum	SCAN
rs10747787	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs10747787	XRCC6BP1	cis	Artery Aorta	GTEx

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58256400-58264600	Weak transcription	Spleen	Spleen
2	chr12:58258600-58261800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr12:58258600-58262000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:58258600-58262200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:58259400-58269600	Weak transcription	Aorta	Aorta
6	chr12:58259600-58261800	Weak transcription	Fetal Stomach	stomach
7	chr12:58259600-58262000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr12:58259600-58262000	Weak transcription	Brain Germinal Matrix	brain
9	chr12:58259600-58262000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr12:58259600-58262000	Weak transcription	Brain Substantia Nigra	brain
11	chr12:58259600-58262200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr12:58259600-58262200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr12:58259600-58262200	Weak transcription	Esophagus	oesophagus
14	chr12:58259600-58262400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr12:58259600-58262600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr12:58259600-58262600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr12:58259600-58262600	Weak transcription	Lung	lung
18	chr12:58259600-58262600	Weak transcription	Pancreas	Pancrea
19	chr12:58259600-58262600	Weak transcription	Psoas Muscle	Psoas
20	chr12:58259600-58262800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr12:58259600-58264000	Enhancers	Placenta	Placenta
22	chr12:58259600-58267800	Weak transcription	Colonic Mucosa	Colon
23	chr12:58259600-58268000	Weak transcription	Left Ventricle	heart
24	chr12:58259800-58260800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr12:58259800-58260800	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr12:58259800-58261800	Weak transcription	Brain Cingulate Gyrus	brain
27	chr12:58259800-58261800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr12:58259800-58262000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr12:58259800-58262000	Weak transcription	Brain Angular Gyrus	brain
30	chr12:58259800-58262000	Weak transcription	Brain Anterior Caudate	brain
31	chr12:58259800-58262000	Weak transcription	Brain Hippocampus Middle	brain
32	chr12:58259800-58262000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr12:58259800-58262000	Weak transcription	Duodenum Mucosa	Duodenum
34	chr12:58259800-58262000	Weak transcription	Fetal Heart	heart
35	chr12:58259800-58262000	Weak transcription	Fetal Kidney	kidney
36	chr12:58259800-58262200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr12:58259800-58262200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr12:58259800-58262200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr12:58259800-58262200	Weak transcription	HSMMtube	muscle
40	chr12:58259800-58262400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr12:58259800-58262600	Weak transcription	HSMM	muscle
42	chr12:58259800-58267600	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr12:58260000-58261800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr12:58260000-58261800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr12:58260000-58261800	Weak transcription	Colon Smooth Muscle	Colon
46	chr12:58260000-58261800	Weak transcription	Fetal Brain Male	brain
47	chr12:58260000-58261800	Weak transcription	Fetal Lung	lung
48	chr12:58260000-58262000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr12:58260000-58262000	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr12:58260000-58262000	Weak transcription	Fetal Muscle Leg	muscle

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