Variant report

Variant	rs12657369
Chromosome Location	chr5:126316926-126316927
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:126315987..126318403-chr5:126363963..126366273,2	K562	blood:
2	chr5:126308755..126310486-chr5:126315115..126318013,2	MCF-7	breast:
3	chr5:126313681..126317112-chr5:126318689..126323055,6	K562	blood:
4	chr5:126315513..126317424-chr5:126323234..126325077,2	K562	blood:

Variant related genes	Relation type
ENSG00000173926	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10053382	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10057084	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];0.98[ASN][1000 genomes]
rs10060747	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10065302	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10067364	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];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10071669	0.93[ASW][hapmap];0.96[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];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1013662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1034844	1.00[CEU][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10463826	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10491284	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10900789	0.96[CEU][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs11241912	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs11241913	0.82[CEU][hapmap];0.83[TSI][hapmap]
rs11949302	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[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];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11956061	0.96[CEU][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs11960799	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[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];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12515192	1.00[CEU][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs12655220	0.82[CEU][hapmap];0.83[TSI][hapmap]
rs12655640	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];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13154281	0.84[EUR][1000 genomes]
rs13189409	0.87[EUR][1000 genomes]
rs2041318	0.85[CEU][hapmap];0.86[CHB][hapmap];0.80[TSI][hapmap]
rs2108458	0.87[EUR][1000 genomes]
rs2108459	0.87[EUR][1000 genomes]
rs2191209	0.92[CEU][hapmap];0.95[CHB][hapmap]
rs2240527	1.00[CEU][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2240528	1.00[CEU][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs248040	0.86[CHB][hapmap]
rs248081	0.84[CEU][hapmap]
rs4131248	0.86[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4380710	0.82[CEU][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs4835921	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];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4835922	0.84[EUR][1000 genomes]
rs4836300	0.85[TSI][hapmap]
rs4836306	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4836307	1.00[CEU][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6860726	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6883871	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6891329	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6891436	1.00[CEU][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6899133	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs727038	0.85[CEU][hapmap];0.90[CHB][hapmap]
rs729607	1.00[CEU][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7706333	1.00[CEU][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs7713933	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7716410	0.96[CEU][hapmap];0.93[TSI][hapmap]
rs7721948	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7731621	0.89[CEU][hapmap];0.95[CHB][hapmap]
rs7731664	0.82[ASN][1000 genomes]
rs7733551	1.00[CEU][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs7736693	1.00[CEU][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs9327424	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9327425	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9327426	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9327428	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];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][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
rs12657369	MARCH3	cis	Muscle Skeletal	GTEx
rs12657369	C5orf63	cis	Artery Tibial	GTEx
rs12657369	C5orf63	cis	Esophagus Muscularis	GTEx
rs12657369	C5orf63	cis	Nerve Tibial	GTEx
rs12657369	C5orf63	cis	Artery Aorta	GTEx
rs12657369	MARCH3	cis	parietal	SCAN
rs12657369	MARCH3	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126306400-126317800	Weak transcription	Ovary	ovary
2	chr5:126306600-126317800	Weak transcription	Aorta	Aorta
3	chr5:126307400-126317800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr5:126308400-126317800	Weak transcription	HSMMtube	muscle
5	chr5:126308400-126328800	Weak transcription	Gastric	stomach
6	chr5:126309000-126319200	Weak transcription	Fetal Intestine Small	intestine
7	chr5:126309000-126331000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr5:126309000-126331600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr5:126309400-126317600	Weak transcription	Brain Substantia Nigra	brain
10	chr5:126309400-126319000	Weak transcription	Spleen	Spleen
11	chr5:126309400-126323000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr5:126309400-126323200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr5:126309400-126323200	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr5:126309400-126334000	Weak transcription	Small Intestine	intestine
15	chr5:126309600-126318800	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr5:126310000-126323400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr5:126312200-126317000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:126312200-126320600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr5:126312600-126317800	Weak transcription	Lung	lung
20	chr5:126312600-126317800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr5:126312600-126319200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr5:126312600-126323400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr5:126312800-126317800	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr5:126312800-126318400	Enhancers	Fetal Heart	heart
25	chr5:126312800-126320600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr5:126312800-126322800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr5:126312800-126331600	Weak transcription	HSMM	muscle
28	chr5:126313800-126317000	Weak transcription	Left Ventricle	heart
29	chr5:126314400-126323400	Enhancers	Primary B cells from peripheral blood	blood
30	chr5:126314600-126317800	Weak transcription	Right Ventricle	heart
31	chr5:126314600-126318000	Weak transcription	Right Atrium	heart
32	chr5:126315000-126317800	Weak transcription	Psoas Muscle	Psoas
33	chr5:126315000-126320000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr5:126315200-126318000	Weak transcription	Primary B cells from cord blood	blood
35	chr5:126315200-126319600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr5:126315200-126320000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr5:126315200-126320600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr5:126315400-126319800	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr5:126316000-126317200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr5:126316000-126318600	Weak transcription	NHLF	lung
41	chr5:126316600-126317200	Enhancers	Fetal Stomach	stomach
42	chr5:126316800-126320600	Enhancers	Fetal Muscle Leg	muscle
43	chr5:126316800-126321800	Enhancers	K562	blood

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