Variant report

Variant	rs9327428
Chromosome Location	chr5:126347544-126347545
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	0.80[EUR][1000 genomes]
rs10053382	1.00[CEU][hapmap];0.87[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];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];0.92[ASN][1000 genomes]
rs10060747	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs10065302	1.00[CEU][hapmap];0.87[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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[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];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1013662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1034844	1.00[CEU][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs10463826	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[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];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10900789	0.96[CEU][hapmap];0.93[TSI][hapmap]
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]
rs11241913	0.82[CEU][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
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];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11956061	0.96[CEU][hapmap];0.91[TSI][hapmap]
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];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12515192	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];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12657369	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]
rs13154281	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13189409	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2041318	0.85[CEU][hapmap];0.85[CHB][hapmap];0.80[TSI][hapmap]
rs2108458	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2108459	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2191209	0.92[CEU][hapmap];0.95[CHB][hapmap];0.82[EUR][1000 genomes]
rs2240527	1.00[CEU][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs2240528	1.00[CEU][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs248040	0.85[CHB][hapmap]
rs248081	0.84[CEU][hapmap]
rs248107	0.89[CEU][hapmap]
rs3936304	0.80[EUR][1000 genomes]
rs3936305	0.80[EUR][1000 genomes]
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];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4380710	0.82[CEU][hapmap];0.85[TSI][hapmap]
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];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4835922	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4836300	0.85[TSI][hapmap]
rs4836306	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4836307	1.00[CEU][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs6595746	0.80[EUR][1000 genomes]
rs6860726	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[ASN][1000 genomes]
rs6875043	0.80[EUR][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];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6891436	1.00[CEU][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs6899133	0.86[AMR][1000 genomes];0.90[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];0.91[EUR][1000 genomes]
rs7706333	1.00[CEU][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.94[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];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7716410	0.96[CEU][hapmap];0.93[TSI][hapmap]
rs7721948	0.87[EUR][1000 genomes]
rs7729349	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7731621	0.89[CEU][hapmap];0.95[CHB][hapmap];0.82[EUR][1000 genomes]
rs7733551	1.00[CEU][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs7736693	1.00[CEU][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9327424	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9327425	0.87[EUR][1000 genomes]
rs9327426	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
rs9327428	MARCH3	cis	parietal	SCAN
rs9327428	C5orf63	cis	Artery Tibial	GTEx
rs9327428	MARCH3	cis	Muscle Skeletal	GTEx
rs9327428	C5orf63	cis	Nerve Tibial	GTEx
rs9327428	C5orf63	cis	Esophagus Muscularis	GTEx
rs9327428	MARCH3	cis	cerebellum	SCAN
rs9327428	C5orf63	cis	Artery Aorta	GTEx

Chromatin state (count:64 , 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	chr5:126340200-126347600	Weak transcription	Primary B cells from cord blood	blood
6	chr5:126340600-126347600	Weak transcription	Primary T cells from cord blood	blood
7	chr5:126340600-126348800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr5:126340800-126347600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr5:126343800-126349600	Enhancers	Fetal Heart	heart
10	chr5:126344600-126349400	Enhancers	HSMMtube	muscle
11	chr5:126345200-126349000	Enhancers	Muscle Satellite Cultured Cells	--
12	chr5:126345200-126349600	Enhancers	Osteobl	bone
13	chr5:126345400-126347800	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr5:126345400-126347800	Enhancers	Right Atrium	heart
15	chr5:126345400-126347800	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr5:126345400-126349000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr5:126345400-126349400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr5:126345400-126350200	Enhancers	Primary B cells from peripheral blood	blood
19	chr5:126345600-126348400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr5:126345600-126348400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr5:126345600-126349400	Enhancers	HSMM	muscle
22	chr5:126345600-126349400	Enhancers	NHDF-Ad	bronchial
23	chr5:126345600-126362400	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr5:126345800-126348200	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr5:126345800-126348800	Weak transcription	Small Intestine	intestine
26	chr5:126345800-126351000	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr5:126346000-126348000	Weak transcription	Brain Cingulate Gyrus	brain
28	chr5:126346000-126348600	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr5:126346000-126349200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr5:126346000-126349400	Enhancers	NH-A	brain
31	chr5:126346200-126351400	Weak transcription	Left Ventricle	heart
32	chr5:126346400-126348600	Weak transcription	Brain Hippocampus Middle	brain
33	chr5:126346600-126347800	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr5:126346800-126347800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr5:126346800-126347800	Enhancers	K562	blood
36	chr5:126346800-126348800	Enhancers	HUVEC	blood vessel
37	chr5:126346800-126349000	Enhancers	NHLF	lung
38	chr5:126346800-126349200	Enhancers	HMEC	breast
39	chr5:126347000-126347800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr5:126347000-126347800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr5:126347000-126347800	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr5:126347000-126347800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr5:126347000-126347800	Enhancers	Brain Anterior Caudate	brain
44	chr5:126347000-126347800	Enhancers	Fetal Muscle Leg	muscle
45	chr5:126347000-126348000	Flanking Active TSS	GM12878-XiMat	blood
46	chr5:126347000-126348600	Enhancers	Brain Angular Gyrus	brain
47	chr5:126347000-126349200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr5:126347000-126349600	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr5:126347000-126349800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr5:126347000-126349800	Weak transcription	Stomach Mucosa	stomach

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