Variant report

Variant	rs2191209
Chromosome Location	chr5:126427546-126427547
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:126426127..126428326-chr5:126431660..126433370,2	MCF-7	breast:
2	chr5:126365094..126367501-chr5:126427423..126429390,2	K562	blood:

Variant related genes	Relation type
ENSG00000173926	Chromatin interaction

Extended variants
information (count: 117 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10035217	0.88[EUR][1000 genomes]
rs10037625	0.84[EUR][1000 genomes]
rs10038644	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10041457	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1004500	0.84[EUR][1000 genomes]
rs10053382	0.93[CEU][hapmap]
rs10057084	0.92[CEU][hapmap];0.95[CHB][hapmap]
rs10060747	0.93[CEU][hapmap]
rs10062622	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10065302	0.93[CEU][hapmap]
rs10067364	0.92[CEU][hapmap];0.95[CHB][hapmap];0.80[EUR][1000 genomes]
rs10071669	0.89[CEU][hapmap];0.95[CHB][hapmap]
rs1013662	0.93[CEU][hapmap];0.95[CHB][hapmap];0.82[EUR][1000 genomes]
rs1034844	0.92[CEU][hapmap]
rs10491284	0.92[CEU][hapmap];0.90[CHB][hapmap]
rs10900789	0.89[CEU][hapmap]
rs11949302	0.89[CEU][hapmap];0.95[CHB][hapmap]
rs11956061	0.89[CEU][hapmap]
rs11960799	0.92[CEU][hapmap];0.95[CHB][hapmap];0.82[EUR][1000 genomes]
rs12515192	0.92[CEU][hapmap]
rs12655640	0.92[CEU][hapmap];0.95[CHB][hapmap];0.80[EUR][1000 genomes]
rs12657369	0.92[CEU][hapmap];0.95[CHB][hapmap]
rs13154281	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13178353	0.81[EUR][1000 genomes]
rs13190493	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1543815	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs173555	0.85[EUR][1000 genomes]
rs1860439	0.85[EUR][1000 genomes]
rs1860440	0.92[EUR][1000 genomes]
rs1860441	0.89[EUR][1000 genomes]
rs193712	0.83[EUR][1000 genomes]
rs2041318	0.92[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2109215	0.82[JPT][hapmap]
rs2240527	0.92[CEU][hapmap]
rs2240528	0.92[CEU][hapmap]
rs2408788	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2408789	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2436437	0.85[EUR][1000 genomes]
rs248040	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs248042	0.89[EUR][1000 genomes]
rs248081	0.88[CEU][hapmap];0.83[JPT][hapmap]
rs248091	0.87[EUR][1000 genomes]
rs248092	0.81[EUR][1000 genomes]
rs248093	0.86[EUR][1000 genomes]
rs248094	0.86[EUR][1000 genomes]
rs248095	0.80[EUR][1000 genomes]
rs248096	0.80[EUR][1000 genomes]
rs248102	0.80[EUR][1000 genomes]
rs248104	0.81[EUR][1000 genomes]
rs248106	0.84[EUR][1000 genomes]
rs248107	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs248108	0.80[EUR][1000 genomes]
rs248111	0.86[EUR][1000 genomes]
rs248112	0.85[EUR][1000 genomes]
rs248114	0.85[EUR][1000 genomes]
rs248115	0.85[EUR][1000 genomes]
rs248116	0.82[EUR][1000 genomes]
rs248117	0.84[EUR][1000 genomes]
rs248119	0.85[EUR][1000 genomes]
rs248122	0.85[EUR][1000 genomes]
rs248124	0.85[EUR][1000 genomes]
rs248125	0.85[EUR][1000 genomes]
rs248127	0.85[EUR][1000 genomes]
rs248128	0.85[EUR][1000 genomes]
rs248129	0.85[EUR][1000 genomes]
rs248131	0.85[EUR][1000 genomes]
rs2532882	0.85[EUR][1000 genomes]
rs2898037	0.81[EUR][1000 genomes]
rs3095137	0.85[EUR][1000 genomes]
rs3097870	0.85[EUR][1000 genomes]
rs3915634	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3936304	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3936305	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4131248	0.89[CEU][hapmap];0.84[CHB][hapmap]
rs4455612	0.91[EUR][1000 genomes]
rs4835921	0.92[CEU][hapmap];0.95[CHB][hapmap]
rs4835922	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4835925	0.85[EUR][1000 genomes]
rs4836307	0.92[CEU][hapmap]
rs4836310	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4836313	0.93[EUR][1000 genomes]
rs4836315	0.85[EUR][1000 genomes]
rs62374042	0.84[EUR][1000 genomes]
rs6860726	0.89[CEU][hapmap];0.95[CHB][hapmap]
rs6864668	0.84[EUR][1000 genomes]
rs6873502	0.93[EUR][1000 genomes]
rs6875043	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6879393	0.84[EUR][1000 genomes]
rs6881948	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6883106	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6883627	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6883871	0.92[CEU][hapmap];0.95[CHB][hapmap];0.82[EUR][1000 genomes]
rs6884988	0.93[EUR][1000 genomes]
rs6887929	0.86[EUR][1000 genomes]
rs6888087	0.85[EUR][1000 genomes]
rs6891436	0.92[CEU][hapmap]
rs6898415	0.84[EUR][1000 genomes]
rs6899133	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs727038	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs729607	0.92[CEU][hapmap]
rs7700812	0.85[EUR][1000 genomes]
rs7706333	0.92[CEU][hapmap]
rs7713933	0.89[CEU][hapmap];0.95[CHB][hapmap]
rs7731621	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7733551	0.92[CEU][hapmap]
rs7734890	0.93[EUR][1000 genomes]
rs7736693	0.92[CEU][hapmap]
rs885699	0.85[EUR][1000 genomes]
rs9327428	0.92[CEU][hapmap];0.95[CHB][hapmap];0.82[EUR][1000 genomes]
rs9687751	0.89[EUR][1000 genomes]
rs9687752	0.89[EUR][1000 genomes]
rs9763733	0.83[EUR][1000 genomes]
rs990743	0.81[EUR][1000 genomes]

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	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
3	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	esv1816248	chr5:126399039-126486539	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2191209	C5orf63	cis	Artery Aorta	GTEx
rs2191209	MARCH3	cis	Muscle Skeletal	GTEx
rs2191209	C5orf63	cis	Artery Tibial	GTEx
rs2191209	C5orf63	cis	Nerve Tibial	GTEx

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126413600-126428000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr5:126416800-126428200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr5:126419400-126428000	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr5:126420600-126427800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr5:126423200-126428200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:126424600-126428000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr5:126424800-126428000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr5:126424800-126428600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr5:126424800-126429800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr5:126425000-126428000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr5:126425000-126428200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr5:126425000-126428200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr5:126425000-126428200	Weak transcription	NH-A	brain
14	chr5:126425200-126428000	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr5:126425200-126428000	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr5:126425200-126428000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr5:126425200-126428000	Weak transcription	NHDF-Ad	bronchial
18	chr5:126425200-126428000	Weak transcription	NHLF	lung
19	chr5:126425200-126428200	Weak transcription	HMEC	breast
20	chr5:126425200-126428200	Weak transcription	HSMMtube	muscle
21	chr5:126425400-126427800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr5:126425400-126429400	Weak transcription	Fetal Intestine Large	intestine
23	chr5:126425400-126429600	Weak transcription	Fetal Intestine Small	intestine
24	chr5:126425400-126432200	Weak transcription	Fetal Thymus	thymus
25	chr5:126427200-126427600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr5:126427200-126430200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr5:126427400-126428800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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