Variant report

Variant	rs12515192
Chromosome Location	chr5:126346950-126346951
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:126284046..126286347-chr5:126345684..126348672,2	K562	blood:
2	chr5:126342663..126348738-chr5:126363680..126367852,7	K562	blood:
3	chr5:126345939..126348448-chr5:126363680..126367241,3	K562	blood:
4	chr5:126340621..126343923-chr5:126345092..126348302,3	K562	blood:
5	chr5:126342423..126345071-chr5:126345507..126348599,3	K562	blood:

Variant related genes	Relation type
ENSG00000173926	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10051184	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10053382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10057084	1.00[CEU][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs10060747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10065302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10067364	1.00[CEU][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs10071669	0.96[CEU][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap]
rs1013662	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1034844	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10463826	0.86[EUR][1000 genomes]
rs10491284	1.00[CEU][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs10491285	0.86[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap]
rs10900789	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11241912	0.96[CEU][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs11241913	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11241916	0.82[EUR][1000 genomes]
rs11949302	0.96[CEU][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap]
rs11956061	0.88[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.82[EUR][1000 genomes]
rs11960799	1.00[CEU][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12655220	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12655640	1.00[CEU][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs12657369	1.00[CEU][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs13154281	0.84[EUR][1000 genomes]
rs13189409	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2041318	0.85[CEU][hapmap]
rs2108458	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2108459	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2191209	0.92[CEU][hapmap]
rs2240527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2240528	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs248081	0.84[CEU][hapmap]
rs248107	0.89[CEU][hapmap]
rs3915634	0.81[EUR][1000 genomes]
rs4131248	0.96[CEU][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap]
rs4380710	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4835921	1.00[CEU][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4835922	0.84[EUR][1000 genomes]
rs4836300	0.87[CHB][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs4836306	0.85[EUR][1000 genomes]
rs4836307	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6595746	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6860726	0.96[CEU][hapmap]
rs6883871	1.00[CEU][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6891436	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[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6899133	0.84[EUR][1000 genomes]
rs727038	0.85[CEU][hapmap]
rs729607	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7449089	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7706333	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7713933	0.96[CEU][hapmap];0.93[TSI][hapmap]
rs7716410	0.88[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap]
rs7721948	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7729349	0.81[EUR][1000 genomes]
rs7731621	0.89[CEU][hapmap]
rs7733551	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7736693	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9327424	0.86[EUR][1000 genomes]
rs9327425	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9327426	0.86[EUR][1000 genomes]
rs9327428	1.00[CEU][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024265	chr5:126213004-126691163	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv869897	chr5:126224358-126445210	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12515192	MARCH3	cis	cerebellum	SCAN
rs12515192	C5orf63	cis	Nerve Tibial	GTEx
rs12515192	MARCH3	cis	parietal	SCAN
rs12515192	C5orf63	cis	Artery Tibial	GTEx
rs12515192	MARCH3	cis	Muscle Skeletal	GTEx
rs12515192	C5orf63	cis	Esophagus Muscularis	GTEx
rs12515192	C5orf63	cis	Artery Aorta	GTEx

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126320800-126356000	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr5:126334400-126363000	Weak transcription	Ovary	ovary
3	chr5:126334600-126351000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr5:126337600-126348600	Weak transcription	Right Ventricle	heart
5	chr5:126338800-126347000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr5:126340200-126347600	Weak transcription	Primary B cells from cord blood	blood
7	chr5:126340600-126347000	Weak transcription	Brain Angular Gyrus	brain
8	chr5:126340600-126347600	Weak transcription	Primary T cells from cord blood	blood
9	chr5:126340600-126348800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr5:126340800-126347600	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr5:126341000-126347000	Weak transcription	Fetal Muscle Leg	muscle
12	chr5:126342600-126347000	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr5:126343000-126347400	Weak transcription	Primary hematopoietic stem cells	blood
14	chr5:126343000-126347400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr5:126343200-126347000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr5:126343800-126349600	Enhancers	Fetal Heart	heart
17	chr5:126344200-126347000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr5:126344400-126347000	Weak transcription	Brain Anterior Caudate	brain
19	chr5:126344400-126347000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr5:126344400-126347000	Weak transcription	Brain Substantia Nigra	brain
21	chr5:126344600-126347000	Weak transcription	Psoas Muscle	Psoas
22	chr5:126344600-126349400	Enhancers	HSMMtube	muscle
23	chr5:126345200-126349000	Enhancers	Muscle Satellite Cultured Cells	--
24	chr5:126345200-126349600	Enhancers	Osteobl	bone
25	chr5:126345400-126347800	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr5:126345400-126347800	Enhancers	Right Atrium	heart
27	chr5:126345400-126347800	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr5:126345400-126349000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr5:126345400-126349400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr5:126345400-126350200	Enhancers	Primary B cells from peripheral blood	blood
31	chr5:126345600-126347400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr5:126345600-126348400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr5:126345600-126348400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr5:126345600-126349400	Enhancers	HSMM	muscle
35	chr5:126345600-126349400	Enhancers	NHDF-Ad	bronchial
36	chr5:126345600-126362400	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr5:126345800-126348200	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr5:126345800-126348800	Weak transcription	Small Intestine	intestine
39	chr5:126345800-126351000	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr5:126346000-126347200	Enhancers	Adipose Nuclei	Adipose
41	chr5:126346000-126348000	Weak transcription	Brain Cingulate Gyrus	brain
42	chr5:126346000-126348600	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr5:126346000-126349200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr5:126346000-126349400	Enhancers	NH-A	brain
45	chr5:126346200-126351400	Weak transcription	Left Ventricle	heart
46	chr5:126346400-126348600	Weak transcription	Brain Hippocampus Middle	brain
47	chr5:126346600-126347000	Enhancers	GM12878-XiMat	blood
48	chr5:126346600-126347800	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr5:126346800-126347000	Enhancers	Stomach Mucosa	stomach
50	chr5:126346800-126347200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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