Variant report

Variant	rs11956061
Chromosome Location	chr5:126245898-126245899
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10053382	0.96[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10057084	0.96[CEU][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs10060747	0.96[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10065302	0.96[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10067364	0.96[CEU][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs10071669	1.00[CEU][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs1013662	0.96[CEU][hapmap]
rs1034844	0.82[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10491284	0.96[CEU][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs10900789	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11241912	1.00[CEU][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs11241913	0.87[CHB][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap]
rs11949302	1.00[CEU][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs11960799	0.96[CEU][hapmap];0.91[TSI][hapmap]
rs12515192	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]
rs12655220	0.87[CHB][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap]
rs12655640	0.96[CEU][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs12657369	0.96[CEU][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs13189409	0.83[EUR][1000 genomes]
rs2041318	0.81[CEU][hapmap]
rs2108458	0.83[EUR][1000 genomes]
rs2108459	0.83[EUR][1000 genomes]
rs2191209	0.89[CEU][hapmap]
rs2240527	0.96[CEU][hapmap];0.87[CHB][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2240528	0.82[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4131248	1.00[CEU][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs4380710	0.87[CHB][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4835921	0.96[CEU][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs4836300	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4836306	0.84[EUR][1000 genomes]
rs4836307	0.88[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6860726	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs6864861	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6883871	0.96[CEU][hapmap];0.91[TSI][hapmap]
rs6891329	0.90[EUR][1000 genomes]
rs6891436	0.94[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6897653	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs727038	0.81[CEU][hapmap]
rs729607	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];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7449089	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7706333	0.88[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.83[EUR][1000 genomes]
rs7713933	0.93[CEU][hapmap];0.91[TSI][hapmap]
rs7716410	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7721948	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7731621	0.85[CEU][hapmap]
rs7731664	0.81[EUR][1000 genomes]
rs7733551	0.94[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7736693	0.88[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.83[EUR][1000 genomes]
rs9327424	0.82[EUR][1000 genomes]
rs9327425	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9327426	0.82[EUR][1000 genomes]
rs9327428	0.96[CEU][hapmap];0.91[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949054	chr5:125918148-126254480	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11956061	MARCH3	cis	cerebellum	SCAN
rs11956061	C5orf63	cis	Artery Aorta	GTEx
rs11956061	MARCH3	cis	Muscle Skeletal	GTEx
rs11956061	C5orf63	cis	Artery Tibial	GTEx
rs11956061	C5orf63	cis	Nerve Tibial	GTEx
rs11956061	C5orf63	cis	Esophagus Muscularis	GTEx
rs11956061	MARCH3	cis	parietal	SCAN
rs11956061	MEGF10	cis	parietal	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126201800-126253400	Weak transcription	A549	lung
2	chr5:126214600-126250400	Weak transcription	Pancreas	Pancrea
3	chr5:126214800-126255200	Weak transcription	Psoas Muscle	Psoas
4	chr5:126229600-126253600	Weak transcription	Brain Anterior Caudate	brain
5	chr5:126231200-126254000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr5:126233800-126256000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr5:126237000-126254000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr5:126237400-126247600	Weak transcription	Fetal Heart	heart
9	chr5:126237800-126256000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr5:126238200-126256000	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr5:126238800-126247400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr5:126238800-126253800	Weak transcription	HSMMtube	muscle
13	chr5:126239000-126250200	Weak transcription	Ovary	ovary
14	chr5:126239200-126247600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr5:126239200-126247600	Weak transcription	Left Ventricle	heart
16	chr5:126239200-126250600	Weak transcription	Right Ventricle	heart
17	chr5:126239200-126250600	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr5:126241200-126250600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr5:126243000-126250400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr5:126243800-126248000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr5:126244000-126253600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr5:126244400-126246200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr5:126244400-126257000	Weak transcription	Fetal Thymus	thymus
24	chr5:126244400-126261200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr5:126245000-126246200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
26	chr5:126245000-126246200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
27	chr5:126245000-126246200	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr5:126245000-126246200	Enhancers	Stomach Mucosa	stomach
29	chr5:126245000-126246400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr5:126245000-126247000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
31	chr5:126245200-126246200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
32	chr5:126245200-126249000	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr5:126245400-126246200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr5:126245400-126246400	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
35	chr5:126245400-126246400	Enhancers	HUVEC	blood vessel
36	chr5:126245400-126247200	Strong transcription	Primary B cells from peripheral blood	blood
37	chr5:126245400-126247600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
38	chr5:126245400-126250400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr5:126245400-126253000	Strong transcription	Fetal Muscle Trunk	muscle
40	chr5:126245400-126253600	Strong transcription	Primary B cells from cord blood	blood
41	chr5:126245400-126256000	Weak transcription	Brain Cingulate Gyrus	brain
42	chr5:126245600-126246200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
43	chr5:126245600-126246200	ZNF genes & repeats	K562	blood
44	chr5:126245600-126246400	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
45	chr5:126245600-126246400	Strong transcription	Primary T cells from cord blood	blood
46	chr5:126245600-126247200	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr5:126245600-126247400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
48	chr5:126245600-126248000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
49	chr5:126245600-126250400	Weak transcription	Aorta	Aorta
50	chr5:126245600-126253600	Strong transcription	HSMM	muscle

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