Variant report

Variant	rs4760341
Chromosome Location	chr12:58281495-58281496
allele	A/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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:58235372..58242263-chr12:58281059..58286678,18	MCF-7	breast:
2	chr12:58273580..58278130-chr12:58279194..58284140,7	MCF-7	breast:
3	chr12:58238917..58240911-chr12:58280507..58282543,2	K562	blood:
4	chr12:58281380..58284295-chr12:58284456..58286004,2	K562	blood:
5	chr12:58272183..58275031-chr12:58279925..58281900,3	K562	blood:
6	chr12:58273430..58275721-chr12:58280183..58281805,2	MCF-7	breast:
7	chr12:58279797..58285277-chr12:58286449..58291551,8	K562	blood:
8	chr12:58238979..58240500-chr12:58280823..58282469,2	K562	blood:
9	chr12:58243942..58248184-chr12:58281468..58284195,4	MCF-7	breast:
10	chr12:58233944..58243826-chr12:58273095..58290464,46	MCF-7	breast:
11	chr12:58227798..58230136-chr12:58279373..58282138,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000175215	Chromatin interaction
ENSG00000245651	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10431552	0.82[JPT][hapmap]
rs10444569	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10747783	0.83[JPT][hapmap]
rs10747786	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10747787	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10783847	0.82[JPT][hapmap]
rs10783850	0.87[JPT][hapmap];0.87[YRI][hapmap];0.84[AMR][1000 genomes]
rs10783851	0.87[JPT][hapmap];0.87[YRI][hapmap];0.84[AMR][1000 genomes]
rs10783853	0.82[CEU][hapmap];0.85[YRI][hapmap]
rs10783854	0.80[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10783855	0.80[CHB][hapmap];0.87[JPT][hapmap];0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10783856	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10877011	0.85[YRI][hapmap]
rs10877012	0.82[JPT][hapmap]
rs10877014	0.82[JPT][hapmap]
rs10877015	0.82[JPT][hapmap]
rs10877016	0.82[JPT][hapmap]
rs10877019	0.82[JPT][hapmap]
rs10877024	0.84[AMR][1000 genomes]
rs10877025	0.84[AMR][1000 genomes]
rs10877026	0.83[AMR][1000 genomes]
rs10877028	0.87[JPT][hapmap]
rs10877029	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10877030	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10877031	0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10877032	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11172333	0.82[JPT][hapmap];0.85[YRI][hapmap]
rs11172335	0.82[JPT][hapmap];0.85[YRI][hapmap]
rs11172344	0.82[JPT][hapmap]
rs11172349	0.82[JPT][hapmap];0.85[YRI][hapmap]
rs11172351	0.82[JPT][hapmap]
rs11172367	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11172368	0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11172369	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11172371	0.82[CHB][hapmap];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11172375	0.81[ASN][1000 genomes]
rs11172378	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs12312955	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12319233	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12426201	0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1599750	0.85[AMR][1000 genomes]
rs1599751	0.87[JPT][hapmap];0.85[AMR][1000 genomes]
rs1599931	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1875124	0.82[JPT][hapmap];0.85[YRI][hapmap]
rs1875125	0.94[JPT][hapmap];0.83[AMR][1000 genomes]
rs1962047	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs2002275	0.82[CHB][hapmap];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2072052	0.85[YRI][hapmap]
rs3751331	0.82[ASN][1000 genomes]
rs3825079	0.82[JPT][hapmap];0.85[YRI][hapmap]
rs4237844	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4646536	0.82[JPT][hapmap]
rs4760171	0.87[JPT][hapmap]
rs4760172	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4760332	0.94[JPT][hapmap]
rs4760339	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.90[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4760340	0.87[CHB][hapmap]
rs5017863	0.89[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs59401446	0.93[ASN][1000 genomes]
rs6581155	0.82[JPT][hapmap]
rs6581157	0.83[ASN][1000 genomes]
rs703842	0.82[JPT][hapmap]
rs7134797	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs724834	0.83[JPT][hapmap]
rs7312623	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7489290	0.85[JPT][hapmap]
rs7969844	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs8181644	0.82[JPT][hapmap]
rs870392	0.94[JPT][hapmap];0.85[YRI][hapmap]
rs871871	0.94[JPT][hapmap]
rs923829	0.83[JPT][hapmap]
rs9645819	0.94[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:16)

SNP	Gene	Cis/trans	Tissue	Source
rs4760341	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs4760341	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs4760341	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs4760341	FAM119B	Cis_1M	lymphoblastoid	RTeQTL
rs4760341	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs4760341	XRCC6BP1	cis	Whole Blood	GTEx
rs4760341	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs4760341	XRCC6BP1	cis	Nerve Tibial	GTEx
rs4760341	XRCC6BP1	cis	Thyroid	GTEx
rs4760341	XRCC6BP1	cis	Artery Aorta	GTEx
rs4760341	XRCC6BP1	cis	Esophagus Muscularis	GTEx
rs4760341	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs4760341	XRCC6BP1	cis	lung	GTEx
rs4760341	XRCC6BP1	cis	Artery Tibial	GTEx
rs4760341	FAM119B	cis	Frontal Cortex	GTEx
rs4760341	FAM119B	cis	Lymphoblastoid	GTEx

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58275400-58281600	Weak transcription	Esophagus	oesophagus
2	chr12:58276000-58281600	Weak transcription	Hela-S3	cervix
3	chr12:58276000-58281800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:58279800-58281800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr12:58279800-58283000	Enhancers	Fetal Lung	lung
6	chr12:58279800-58287000	Enhancers	Fetal Stomach	stomach
7	chr12:58280200-58281600	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr12:58280200-58281800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:58280200-58287400	Enhancers	Fetal Muscle Leg	muscle
10	chr12:58280400-58281600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr12:58280400-58281600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr12:58280400-58281600	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr12:58280400-58281600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr12:58280400-58281600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr12:58280400-58281600	Enhancers	NHDF-Ad	bronchial
16	chr12:58280400-58281600	Enhancers	NHLF	lung
17	chr12:58280400-58281800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr12:58280400-58281800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:58280400-58281800	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr12:58280400-58281800	Enhancers	HMEC	breast
21	chr12:58280400-58282000	Enhancers	Ovary	ovary
22	chr12:58280400-58282000	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr12:58280400-58284400	Enhancers	Right Atrium	heart
24	chr12:58280400-58284800	Enhancers	Lung	lung
25	chr12:58280400-58288000	Enhancers	Fetal Intestine Large	intestine
26	chr12:58280600-58281600	Weak transcription	Brain Hippocampus Middle	brain
27	chr12:58280600-58281600	Enhancers	Stomach Smooth Muscle	stomach
28	chr12:58280600-58281800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:58280600-58281800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr12:58280600-58282400	Enhancers	Colonic Mucosa	Colon
31	chr12:58280600-58284800	Enhancers	Stomach Mucosa	stomach
32	chr12:58280800-58281600	Weak transcription	Fetal Intestine Small	intestine
33	chr12:58280800-58281600	Weak transcription	Small Intestine	intestine
34	chr12:58280800-58281800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr12:58280800-58281800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr12:58280800-58281800	Weak transcription	Psoas Muscle	Psoas
37	chr12:58280800-58282200	Enhancers	Aorta	Aorta
38	chr12:58280800-58284800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr12:58281000-58288000	Enhancers	Fetal Muscle Trunk	muscle
40	chr12:58281200-58281600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr12:58281200-58281600	Enhancers	Osteobl	bone
42	chr12:58281200-58281800	Enhancers	NHEK	skin
43	chr12:58281200-58282000	Enhancers	NH-A	brain
44	chr12:58281200-58283000	Enhancers	Spleen	Spleen
45	chr12:58281200-58283200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr12:58281400-58281600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr12:58281400-58281800	Enhancers	HSMMtube	muscle
48	chr12:58281400-58282000	Enhancers	Brain Substantia Nigra	brain
49	chr12:58281400-58282200	Enhancers	Rectal Mucosa Donor 29	rectum
50	chr12:58281400-58283000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

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