Variant report

Variant	rs6860726
Chromosome Location	chr5:126259178-126259179
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:126258710..126261144-chr5:126262419..126265615,3	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10053382	0.96[CEU][hapmap]
rs10057084	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];0.89[ASN][1000 genomes]
rs10060747	0.96[CEU][hapmap]
rs10065302	0.96[CEU][hapmap]
rs10067364	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[ASN][1000 genomes]
rs10071669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1013662	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.82[ASN][1000 genomes]
rs1034844	0.96[CEU][hapmap]
rs10463826	0.81[EUR][1000 genomes]
rs10491284	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10900789	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs11241912	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11949302	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11956061	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs11960799	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[ASN][1000 genomes]
rs12515192	0.96[CEU][hapmap]
rs12655640	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12657369	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]
rs2041318	0.81[CEU][hapmap];0.86[CHB][hapmap]
rs2191209	0.89[CEU][hapmap];0.95[CHB][hapmap]
rs2240527	0.96[CEU][hapmap]
rs2240528	0.96[CEU][hapmap]
rs4131248	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4835921	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4836300	0.82[CEU][hapmap]
rs4836306	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4836307	0.96[CEU][hapmap]
rs6883871	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[ASN][1000 genomes]
rs6891329	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6891436	0.96[CEU][hapmap]
rs727038	0.81[CEU][hapmap];0.90[CHB][hapmap]
rs729607	0.96[CEU][hapmap]
rs7706333	0.96[CEU][hapmap]
rs7713933	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap]
rs7716410	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs7731621	0.86[CEU][hapmap];0.95[CHB][hapmap]
rs7731664	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7733551	0.96[CEU][hapmap]
rs7736693	0.96[CEU][hapmap]
rs9327424	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9327426	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9327428	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534292	chr5:125993451-126259315	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	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
3	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6860726	MARCH3	cis	Muscle Skeletal	GTEx
rs6860726	C5orf63	cis	Nerve Tibial	GTEx
rs6860726	C5orf63	cis	Artery Aorta	GTEx
rs6860726	C5orf63	cis	Artery Tibial	GTEx
rs6860726	C5orf63	cis	Esophagus Muscularis	GTEx

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126244400-126261200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:126246200-126259800	Weak transcription	Fetal Kidney	kidney
3	chr5:126253600-126300400	Weak transcription	Primary B cells from cord blood	blood
4	chr5:126254000-126261800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr5:126254000-126277800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr5:126254000-126278800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr5:126255400-126272400	Weak transcription	HSMM	muscle
8	chr5:126255600-126263200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr5:126255600-126272400	Weak transcription	HSMMtube	muscle
10	chr5:126256200-126261000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr5:126256400-126259400	Enhancers	Left Ventricle	heart
12	chr5:126257200-126262000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr5:126257200-126267800	Weak transcription	Psoas Muscle	Psoas
14	chr5:126257400-126260200	Weak transcription	Brain Anterior Caudate	brain
15	chr5:126257400-126261800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr5:126257400-126263200	Weak transcription	Brain Substantia Nigra	brain
17	chr5:126257600-126259200	Enhancers	K562	blood
18	chr5:126257800-126262800	Enhancers	Fetal Heart	heart
19	chr5:126257800-126267800	Weak transcription	Primary B cells from peripheral blood	blood
20	chr5:126257800-126274000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr5:126258000-126259600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr5:126258000-126259800	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr5:126258000-126260000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:126258000-126260600	Weak transcription	Brain Germinal Matrix	brain
25	chr5:126258000-126261400	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr5:126258000-126261800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr5:126258000-126261800	Weak transcription	Right Atrium	heart
28	chr5:126258000-126262000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr5:126258000-126262000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr5:126258000-126262000	Weak transcription	Right Ventricle	heart
31	chr5:126258000-126263200	Weak transcription	Fetal Muscle Trunk	muscle
32	chr5:126258000-126263200	Weak transcription	Fetal Muscle Leg	muscle
33	chr5:126258000-126266600	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr5:126258000-126266600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr5:126258000-126274800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr5:126258200-126261600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr5:126258200-126266600	Weak transcription	HUES64 Cell Line	embryonic stem cell

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