Variant report

Variant	rs7312623
Chromosome Location	chr12:58262523-58262524
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:58237087..58244044-chr12:58260690..58267738,8	K562	blood:
2	chr12:58258786..58263861-chr12:58273729..58277386,6	MCF-7	breast:
3	chr12:58238079..58239938-chr12:58262220..58264742,2	K562	blood:
4	chr12:58262380..58265069-chr12:58266414..58270393,4	K562	blood:
5	chr12:58259629..58265686-chr12:58266089..58272179,8	K562	blood:
6	chr12:58262266..58264852-chr12:58270449..58272179,2	K562	blood:
7	chr12:58259698..58262580-chr5:154319260..154321205,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175215	Chromatin interaction
ENSG00000082515	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10431552	0.83[JPT][hapmap]
rs10444569	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10747783	0.83[JPT][hapmap]
rs10747784	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10747786	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]
rs10747787	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]
rs10783847	0.83[JPT][hapmap]
rs10783848	0.80[JPT][hapmap]
rs10783850	0.89[ASW][hapmap];0.80[CHD][hapmap];0.83[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.87[AMR][1000 genomes]
rs10783851	0.89[ASW][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.87[AMR][1000 genomes]
rs10783854	0.87[JPT][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10783855	0.87[CHD][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap];0.91[YRI][hapmap];0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10783856	0.89[AMR][1000 genomes];0.83[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]
rs10877024	0.87[AMR][1000 genomes]
rs10877025	0.87[AMR][1000 genomes]
rs10877026	0.86[AMR][1000 genomes]
rs10877028	0.87[CHD][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.83[TSI][hapmap]
rs10877029	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]
rs10877030	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]
rs10877031	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10877032	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[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]
rs11172362	0.83[AMR][1000 genomes]
rs11172367	1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11172368	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11172369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172371	0.82[CHB][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11172375	0.81[ASN][1000 genomes]
rs11172378	0.82[CHB][hapmap];0.90[CHD][hapmap];0.84[MEX][hapmap];0.81[ASN][1000 genomes]
rs12312955	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12319233	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12426201	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1599750	0.87[CHD][hapmap];0.80[TSI][hapmap];0.89[AMR][1000 genomes]
rs1599751	0.83[CHD][hapmap];0.87[JPT][hapmap];0.88[MEX][hapmap];0.83[TSI][hapmap];0.89[AMR][1000 genomes]
rs1599931	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1875124	0.83[JPT][hapmap]
rs1875125	0.94[JPT][hapmap];0.86[AMR][1000 genomes]
rs1962047	0.82[CHB][hapmap];0.93[CHD][hapmap];0.84[MEX][hapmap];0.83[ASN][1000 genomes]
rs2002275	0.96[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3751331	0.83[ASN][1000 genomes]
rs3825079	0.83[JPT][hapmap]
rs4237844	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4237845	0.93[CHD][hapmap]
rs4630335	0.84[CHD][hapmap]
rs4646536	0.83[JPT][hapmap]
rs4760171	0.87[JPT][hapmap]
rs4760172	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];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4760332	0.81[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.82[AMR][1000 genomes]
rs4760335	0.81[AMR][1000 genomes]
rs4760339	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4760340	0.87[CHB][hapmap];0.97[CHD][hapmap]
rs4760341	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs5017863	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59401446	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6581155	0.83[JPT][hapmap]
rs6581157	0.83[ASN][1000 genomes]
rs703842	0.83[JPT][hapmap]
rs7134797	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs724834	0.83[JPT][hapmap]
rs7489290	0.92[JPT][hapmap];0.81[AMR][1000 genomes]
rs7954957	0.93[CHD][hapmap]
rs7969844	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7971877	0.83[CHD][hapmap]
rs8181644	0.83[JPT][hapmap]
rs870392	0.83[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.82[AMR][1000 genomes]
rs871871	0.83[CHD][hapmap];0.94[JPT][hapmap]
rs923829	0.83[JPT][hapmap]
rs9645819	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[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:15)

SNP	Gene	Cis/trans	Tissue	Source
rs7312623	TSFM	cis	lymphoblastoid	seeQTL
rs7312623	METTL21B	cis	lung	GTEx
rs7312623	XRCC6BP1	cis	lymphoblastoid	seeQTL
rs7312623	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs7312623	FAM119B	cis	cerebellum	SCAN
rs7312623	XRCC6BP1	cis	Whole Blood	GTEx
rs7312623	CDK2	cis	parietal	SCAN
rs7312623	XRCC6BP1	cis	Heart Left Ventricle	GTEx
rs7312623	XRCC6BP1	Cis_1M	lymphoblastoid	RTeQTL
rs7312623	XRCC6BP1	cis	Skin Sun Exposed Lower leg	GTEx
rs7312623	XRCC6BP1	cis	Adipose Subcutaneous	GTEx
rs7312623	TSFM	cis	parietal	SCAN
rs7312623	FAM119B	cis	lymphoblastoid	seeQTL
rs7312623	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs7312623	XRCC6BP1	cis	Artery Tibial	GTEx

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58256400-58264600	Weak transcription	Spleen	Spleen
2	chr12:58259400-58269600	Weak transcription	Aorta	Aorta
3	chr12:58259600-58262600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:58259600-58262600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr12:58259600-58262600	Weak transcription	Lung	lung
6	chr12:58259600-58262600	Weak transcription	Pancreas	Pancrea
7	chr12:58259600-58262600	Weak transcription	Psoas Muscle	Psoas
8	chr12:58259600-58262800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr12:58259600-58264000	Enhancers	Placenta	Placenta
10	chr12:58259600-58267800	Weak transcription	Colonic Mucosa	Colon
11	chr12:58259600-58268000	Weak transcription	Left Ventricle	heart
12	chr12:58259800-58262600	Weak transcription	HSMM	muscle
13	chr12:58259800-58267600	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr12:58260600-58262600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr12:58260600-58263000	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr12:58261600-58262600	Weak transcription	Right Atrium	heart
17	chr12:58261800-58262800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr12:58261800-58263000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr12:58261800-58264000	Enhancers	Brain Cingulate Gyrus	brain
20	chr12:58261800-58264400	Enhancers	Colon Smooth Muscle	Colon
21	chr12:58261800-58264400	Enhancers	Fetal Muscle Trunk	muscle
22	chr12:58261800-58264400	Enhancers	Fetal Stomach	stomach
23	chr12:58261800-58264600	Enhancers	Fetal Lung	lung
24	chr12:58261800-58265200	Enhancers	Fetal Brain Male	brain
25	chr12:58262000-58262600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
26	chr12:58262000-58262600	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr12:58262000-58262800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr12:58262000-58262800	Enhancers	Brain Substantia Nigra	brain
29	chr12:58262000-58262800	Enhancers	Duodenum Mucosa	Duodenum
30	chr12:58262000-58262800	Enhancers	Skeletal Muscle Male	skeletal muscle
31	chr12:58262000-58262800	Enhancers	NHDF-Ad	bronchial
32	chr12:58262000-58263000	Enhancers	Fetal Brain Female	brain
33	chr12:58262000-58263200	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr12:58262000-58263400	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr12:58262000-58264000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr12:58262000-58264200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr12:58262000-58264200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr12:58262000-58264400	Enhancers	Brain Angular Gyrus	brain
39	chr12:58262000-58264600	Enhancers	Fetal Muscle Leg	muscle
40	chr12:58262200-58262800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr12:58262200-58262800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr12:58262200-58262800	Enhancers	Adipose Nuclei	Adipose
43	chr12:58262200-58262800	Enhancers	Esophagus	oesophagus
44	chr12:58262200-58262800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
45	chr12:58262200-58263000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr12:58262200-58263000	Enhancers	Fetal Intestine Small	intestine
47	chr12:58262200-58263200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr12:58262200-58263200	Flanking Active TSS	Rectal Smooth Muscle	rectum
49	chr12:58262200-58263400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr12:58262200-58263400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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