Variant report

Variant	rs11241912
Chromosome Location	chr5:126218717-126218718
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:126218400-126221513	K562	blood:	n/a	n/a
2	HCFC1	chr5:126218701-126218717	K562	blood:	n/a	n/a
3	CUX1	chr5:126218622-126218769	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:126216405..126219014-chr5:126341238..126343665,2	K562	blood:
2	chr5:126217612..126219765-chr5:126223555..126225537,2	MCF-7	breast:
3	chr5:126211823..126213639-chr5:126216615..126218789,2	MCF-7	breast:
4	chr5:126218335..126221734-chr5:126363299..126367120,5	K562	blood:

No data

Variant related genes	Relation type
MARCH3	TF binding region
ENSG00000173926	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10053382	0.96[CEU][hapmap]
rs10057084	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]
rs10060747	0.96[CEU][hapmap]
rs10065302	0.96[CEU][hapmap]
rs10067364	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];0.81[EUR][1000 genomes]
rs10071669	0.86[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1013662	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs1034844	0.96[CEU][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap]
rs10491284	0.96[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs10900789	1.00[CEU][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs11241913	0.83[TSI][hapmap]
rs11949302	0.86[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11956061	1.00[CEU][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs11960799	0.96[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs12515192	0.96[CEU][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs12655220	0.82[MEX][hapmap];0.83[TSI][hapmap]
rs12655640	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];0.81[EUR][1000 genomes]
rs12657369	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]
rs2240527	0.96[CEU][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap]
rs2240528	0.96[CEU][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap]
rs4131248	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4380710	0.82[MEX][hapmap];0.85[TSI][hapmap]
rs4835921	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs4836300	0.82[CEU][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs4836306	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4836307	0.96[CEU][hapmap];0.93[TSI][hapmap]
rs6860726	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6864861	0.92[EUR][1000 genomes]
rs6883871	0.96[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs6891329	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6891436	0.96[CEU][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs729607	0.96[CEU][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs7706333	0.96[CEU][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs7713933	0.92[CEU][hapmap];0.90[CHB][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap]
rs7716410	1.00[CEU][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs7731664	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7733551	0.96[CEU][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs7736693	0.96[CEU][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap]
rs9327424	0.83[EUR][1000 genomes]
rs9327426	0.83[EUR][1000 genomes]
rs9327428	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]

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	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs11241912	C5orf63	cis	Nerve Tibial	GTEx
rs11241912	C5orf63	cis	Artery Tibial	GTEx
rs11241912	MARCH3	cis	cerebellum	SCAN
rs11241912	MARCH3	cis	Muscle Skeletal	GTEx
rs11241912	MEGF10	cis	parietal	SCAN
rs11241912	MARCH3	cis	parietal	SCAN
rs11241912	C5orf63	cis	Artery Aorta	GTEx
rs11241912	C5orf63	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126201800-126253400	Weak transcription	A549	lung
2	chr5:126205200-126219200	Weak transcription	Osteobl	bone
3	chr5:126205200-126245600	Weak transcription	Duodenum Mucosa	Duodenum
4	chr5:126205400-126219200	Weak transcription	Brain Substantia Nigra	brain
5	chr5:126205400-126219600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr5:126205400-126220200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr5:126205400-126220800	Weak transcription	Thymus	Thymus
8	chr5:126205400-126221400	Weak transcription	Fetal Thymus	thymus
9	chr5:126205400-126245600	Weak transcription	Primary hematopoietic stem cells	blood
10	chr5:126205600-126220200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr5:126205600-126223400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr5:126205600-126238200	Weak transcription	Primary T cells from cord blood	blood
13	chr5:126206400-126220400	Weak transcription	Lung	lung
14	chr5:126206800-126220000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr5:126207600-126221600	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr5:126209000-126219600	Weak transcription	HSMMtube	muscle
17	chr5:126210600-126223400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr5:126211200-126219600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr5:126211200-126221800	Weak transcription	Fetal Intestine Small	intestine
20	chr5:126211200-126231600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr5:126211600-126220200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr5:126211800-126223400	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr5:126212000-126236800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr5:126213600-126219200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr5:126213800-126219200	Weak transcription	HUVEC	blood vessel
26	chr5:126214000-126219400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr5:126214200-126219200	Weak transcription	HSMM	muscle
28	chr5:126214200-126237400	Weak transcription	Fetal Brain Female	brain
29	chr5:126214200-126238600	Weak transcription	Fetal Muscle Leg	muscle
30	chr5:126214200-126238600	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr5:126214200-126245400	Weak transcription	Fetal Muscle Trunk	muscle
32	chr5:126214600-126219600	Weak transcription	Ovary	ovary
33	chr5:126214600-126220200	Weak transcription	Left Ventricle	heart
34	chr5:126214600-126232000	Weak transcription	Primary B cells from peripheral blood	blood
35	chr5:126214600-126245200	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr5:126214600-126250400	Weak transcription	Pancreas	Pancrea
37	chr5:126214800-126219200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr5:126214800-126255200	Weak transcription	Psoas Muscle	Psoas
39	chr5:126215000-126219200	Weak transcription	Fetal Heart	heart
40	chr5:126215400-126245000	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr5:126215600-126220200	Weak transcription	Right Ventricle	heart
42	chr5:126216400-126219200	Genic enhancers	K562	blood
43	chr5:126217400-126218800	Strong transcription	Primary B cells from cord blood	blood

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