Variant report

Variant	rs3915634
Chromosome Location	chr5:126430990-126430991
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 123 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs10035217	0.85[EUR][1000 genomes]
rs10037625	0.81[EUR][1000 genomes]
rs10038644	0.90[EUR][1000 genomes]
rs10041457	0.90[EUR][1000 genomes]
rs1004500	0.81[EUR][1000 genomes]
rs10053382	0.93[CEU][hapmap]
rs10057084	0.92[CEU][hapmap]
rs10060747	0.93[CEU][hapmap]
rs10062622	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10065302	0.93[CEU][hapmap]
rs10067364	0.92[CEU][hapmap]
rs10071669	0.89[CEU][hapmap]
rs1013662	0.93[CEU][hapmap]
rs1034844	0.92[CEU][hapmap]
rs10491284	0.92[CEU][hapmap]
rs108558	0.80[EUR][1000 genomes]
rs10900789	0.89[CEU][hapmap]
rs11241916	0.81[EUR][1000 genomes]
rs11949302	0.89[CEU][hapmap]
rs11956061	0.89[CEU][hapmap]
rs11960799	0.92[CEU][hapmap]
rs12515192	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs12655640	0.92[CEU][hapmap]
rs12657369	0.92[CEU][hapmap]
rs13154281	0.84[EUR][1000 genomes]
rs13189409	0.82[EUR][1000 genomes]
rs13190493	0.90[EUR][1000 genomes]
rs1543815	0.91[EUR][1000 genomes]
rs173555	0.81[EUR][1000 genomes]
rs1860439	0.81[EUR][1000 genomes]
rs1860440	0.89[EUR][1000 genomes]
rs1860441	0.86[EUR][1000 genomes]
rs193712	0.80[EUR][1000 genomes]
rs2041318	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs2108458	0.82[EUR][1000 genomes]
rs2108459	0.82[EUR][1000 genomes]
rs2109215	0.81[CEU][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs2191209	0.93[CEU][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2240527	0.92[CEU][hapmap]
rs2240528	0.92[CEU][hapmap]
rs2408788	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2408789	0.91[EUR][1000 genomes]
rs2408790	0.86[EUR][1000 genomes]
rs2436437	0.81[EUR][1000 genomes]
rs248042	0.86[EUR][1000 genomes]
rs248062	0.83[EUR][1000 genomes]
rs248081	0.89[CEU][hapmap]
rs248091	0.83[EUR][1000 genomes]
rs248092	0.88[EUR][1000 genomes]
rs248093	0.82[EUR][1000 genomes]
rs248094	0.82[EUR][1000 genomes]
rs248095	0.87[EUR][1000 genomes]
rs248096	0.87[EUR][1000 genomes]
rs248101	0.86[EUR][1000 genomes]
rs248102	0.87[EUR][1000 genomes]
rs248105	0.81[EUR][1000 genomes]
rs248106	0.82[EUR][1000 genomes]
rs248107	0.93[CEU][hapmap];0.87[EUR][1000 genomes]
rs248108	0.87[EUR][1000 genomes]
rs248109	0.80[EUR][1000 genomes]
rs248111	0.82[EUR][1000 genomes]
rs248112	0.81[EUR][1000 genomes]
rs248114	0.81[EUR][1000 genomes]
rs248115	0.81[EUR][1000 genomes]
rs248117	0.81[EUR][1000 genomes]
rs248119	0.81[EUR][1000 genomes]
rs248122	0.81[EUR][1000 genomes]
rs248124	0.81[EUR][1000 genomes]
rs248125	0.81[EUR][1000 genomes]
rs248127	0.81[EUR][1000 genomes]
rs248128	0.81[EUR][1000 genomes]
rs248129	0.81[EUR][1000 genomes]
rs248131	0.81[EUR][1000 genomes]
rs2532882	0.81[EUR][1000 genomes]
rs3095137	0.81[EUR][1000 genomes]
rs3097870	0.81[EUR][1000 genomes]
rs3936304	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3936305	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4131248	0.89[CEU][hapmap]
rs4455612	0.87[EUR][1000 genomes]
rs4835921	0.92[CEU][hapmap]
rs4835922	0.86[EUR][1000 genomes]
rs4835925	0.81[EUR][1000 genomes]
rs4836307	0.92[CEU][hapmap]
rs4836310	0.89[EUR][1000 genomes]
rs4836313	0.89[EUR][1000 genomes]
rs4836315	0.81[EUR][1000 genomes]
rs62374042	0.81[EUR][1000 genomes]
rs6859962	0.86[EUR][1000 genomes]
rs6860726	0.89[CEU][hapmap]
rs6864668	0.81[EUR][1000 genomes]
rs6873502	0.90[EUR][1000 genomes]
rs6875043	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6879393	0.81[EUR][1000 genomes]
rs6881948	0.90[EUR][1000 genomes]
rs6883106	0.91[EUR][1000 genomes]
rs6883627	0.90[EUR][1000 genomes]
rs6883672	0.86[EUR][1000 genomes]
rs6883871	0.92[CEU][hapmap]
rs6884988	0.89[EUR][1000 genomes]
rs6887929	0.83[EUR][1000 genomes]
rs6888087	0.81[EUR][1000 genomes]
rs6891436	0.92[CEU][hapmap]
rs6898415	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6899133	0.81[EUR][1000 genomes]
rs727038	0.92[CEU][hapmap];0.91[JPT][hapmap];0.90[EUR][1000 genomes]
rs729607	0.92[CEU][hapmap]
rs7700812	0.81[EUR][1000 genomes]
rs7706333	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs7713933	0.89[CEU][hapmap]
rs7731621	0.96[CEU][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7733551	0.92[CEU][hapmap]
rs7734890	0.89[EUR][1000 genomes]
rs7736693	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs885699	0.81[EUR][1000 genomes]
rs9327428	0.92[CEU][hapmap]
rs9687751	0.86[EUR][1000 genomes]
rs9687752	0.86[EUR][1000 genomes]
rs9763733	0.80[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3915634	MARCH3	cis	Muscle Skeletal	GTEx
rs3915634	C5orf63	cis	Artery Tibial	GTEx
rs3915634	C5orf63	cis	Nerve Tibial	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126425400-126432200	Weak transcription	Fetal Thymus	thymus
2	chr5:126428000-126432400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr5:126428000-126434000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr5:126428800-126431400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr5:126428800-126431400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr5:126428800-126432200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr5:126428800-126433200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:126429000-126431000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr5:126429400-126431000	Enhancers	Brain Anterior Caudate	brain
10	chr5:126429400-126431200	Enhancers	Fetal Intestine Large	intestine
11	chr5:126429600-126431200	Enhancers	Brain Substantia Nigra	brain
12	chr5:126429600-126431400	Enhancers	Fetal Intestine Small	intestine
13	chr5:126429800-126431200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr5:126430000-126431200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr5:126430000-126433400	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr5:126430200-126431600	Enhancers	Brain Germinal Matrix	brain
17	chr5:126430200-126432200	Enhancers	H1 Cell Line	embryonic stem cell
18	chr5:126430200-126432200	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr5:126430200-126433400	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr5:126430200-126433400	Enhancers	Fetal Muscle Leg	muscle
21	chr5:126430200-126433600	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr5:126430200-126433800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr5:126430200-126434200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr5:126430400-126431000	Enhancers	Fetal Brain Male	brain
25	chr5:126430400-126431400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr5:126430400-126433400	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr5:126430600-126431400	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr5:126430800-126431200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr5:126430800-126431200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr5:126430800-126431400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr5:126430800-126431400	Enhancers	H9 Cell Line	embryonic stem cell

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