Variant report

Variant	rs3936305
Chromosome Location	chr5:126433164-126433165
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:126431823..126435408-chr5:126435480..126438408,3	MCF-7	breast:
2	chr5:126426127..126428326-chr5:126431660..126433370,2	MCF-7	breast:

Extended variants
information (count: 122 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10035217	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10037625	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10038644	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10041457	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1004500	0.88[EUR][1000 genomes]
rs10053382	0.85[CEU][hapmap]
rs10057084	0.85[CEU][hapmap];0.90[CHB][hapmap];0.80[GIH][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs10060747	0.85[CEU][hapmap]
rs10062622	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10065302	0.85[CEU][hapmap]
rs10067364	0.85[CEU][hapmap];0.90[CHB][hapmap];0.80[GIH][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs10071669	0.81[CEU][hapmap];0.90[CHB][hapmap];0.80[GIH][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs1013662	0.85[CEU][hapmap];0.90[CHB][hapmap];0.80[EUR][1000 genomes]
rs1034844	0.85[CEU][hapmap]
rs10491284	0.85[CEU][hapmap];0.85[CHB][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]
rs10900789	0.81[CEU][hapmap]
rs11949302	0.81[CEU][hapmap];0.90[CHB][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs11956061	0.81[CEU][hapmap]
rs11960799	0.85[CEU][hapmap];0.90[CHB][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs12515192	0.85[CEU][hapmap]
rs12655640	0.85[CEU][hapmap];0.90[CHB][hapmap];0.80[GIH][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs12657369	0.85[CEU][hapmap];0.90[CHB][hapmap];0.80[GIH][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs13154281	0.87[EUR][1000 genomes]
rs13178353	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13190493	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1543815	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs173555	0.89[EUR][1000 genomes]
rs1860439	0.89[EUR][1000 genomes]
rs1860440	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1860441	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs193712	0.87[EUR][1000 genomes]
rs2041318	1.00[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2109215	0.82[CEU][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.83[EUR][1000 genomes]
rs2191209	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2240527	0.85[CEU][hapmap]
rs2240528	0.85[CEU][hapmap]
rs2408788	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2408789	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2408790	0.83[EUR][1000 genomes]
rs2436437	0.89[EUR][1000 genomes]
rs248040	0.85[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap]
rs248042	0.93[EUR][1000 genomes]
rs248081	1.00[CEU][hapmap];0.82[JPT][hapmap]
rs248091	0.91[EUR][1000 genomes]
rs248092	0.85[EUR][1000 genomes]
rs248093	0.90[EUR][1000 genomes]
rs248094	0.90[EUR][1000 genomes]
rs248095	0.84[EUR][1000 genomes]
rs248096	0.84[EUR][1000 genomes]
rs248101	0.83[EUR][1000 genomes]
rs248102	0.84[EUR][1000 genomes]
rs248104	0.85[EUR][1000 genomes]
rs248106	0.88[EUR][1000 genomes]
rs248107	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs248108	0.84[EUR][1000 genomes]
rs248111	0.90[EUR][1000 genomes]
rs248112	0.89[EUR][1000 genomes]
rs248113	0.81[CEU][hapmap]
rs248114	0.89[EUR][1000 genomes]
rs248115	0.89[EUR][1000 genomes]
rs248116	0.86[EUR][1000 genomes]
rs248117	0.88[EUR][1000 genomes]
rs248119	0.89[EUR][1000 genomes]
rs248122	0.89[EUR][1000 genomes]
rs248124	0.89[EUR][1000 genomes]
rs248125	0.89[EUR][1000 genomes]
rs248127	0.89[EUR][1000 genomes]
rs248128	0.89[EUR][1000 genomes]
rs248129	0.89[EUR][1000 genomes]
rs248131	0.89[EUR][1000 genomes]
rs2532882	0.89[EUR][1000 genomes]
rs2898037	0.84[EUR][1000 genomes]
rs3095137	0.89[EUR][1000 genomes]
rs3097870	0.89[EUR][1000 genomes]
rs3915634	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3936304	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4131248	0.81[CEU][hapmap];0.87[MEX][hapmap]
rs4455612	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4835921	0.85[CEU][hapmap];0.90[CHB][hapmap];0.80[GIH][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]
rs4835922	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4835925	0.89[EUR][1000 genomes]
rs4836307	0.85[CEU][hapmap]
rs4836310	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4836313	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4836315	0.89[EUR][1000 genomes]
rs62374042	0.88[EUR][1000 genomes]
rs6859962	0.83[EUR][1000 genomes]
rs6860726	0.81[CEU][hapmap];0.90[CHB][hapmap]
rs6864668	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6873502	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6875043	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6879393	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6881948	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6883106	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6883627	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6883672	0.83[EUR][1000 genomes]
rs6883871	0.85[CEU][hapmap];0.90[CHB][hapmap];0.80[GIH][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs6884988	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6887929	0.90[EUR][1000 genomes]
rs6888087	0.89[EUR][1000 genomes]
rs6891436	0.85[CEU][hapmap]
rs6898415	0.84[EUR][1000 genomes]
rs6899133	0.84[EUR][1000 genomes]
rs727038	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs729607	0.85[CEU][hapmap]
rs7700812	0.89[EUR][1000 genomes]
rs7706333	0.85[CEU][hapmap]
rs7713933	0.81[CEU][hapmap];0.89[CHB][hapmap];0.81[TSI][hapmap]
rs7731621	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7733551	0.85[CEU][hapmap]
rs7734890	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7736693	0.85[CEU][hapmap]
rs885699	0.89[EUR][1000 genomes]
rs9327428	0.85[CEU][hapmap];0.90[CHB][hapmap];0.80[GIH][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs9687751	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9687752	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9763733	0.87[EUR][1000 genomes]
rs990743	0.85[EUR][1000 genomes];0.81[ASN][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3936305	C5orf63	cis	Artery Tibial	GTEx
rs3936305	C5orf63	cis	Esophagus Muscularis	GTEx
rs3936305	C5orf63	cis	Artery Aorta	GTEx
rs3936305	MARCH3	cis	Muscle Skeletal	GTEx
rs3936305	MARCH3	cis	cerebellum	SCAN
rs3936305	C5orf63	cis	Nerve Tibial	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126428000-126434000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr5:126428800-126433200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:126430000-126433400	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr5:126430200-126433400	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr5:126430200-126433400	Enhancers	Fetal Muscle Leg	muscle
6	chr5:126430200-126433600	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr5:126430200-126433800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr5:126430200-126434200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr5:126430400-126433400	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr5:126431200-126433400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr5:126431200-126437000	Weak transcription	Fetal Intestine Large	intestine
12	chr5:126431400-126433800	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr5:126431400-126435800	Weak transcription	Fetal Intestine Small	intestine
14	chr5:126431800-126433400	Enhancers	H9 Cell Line	embryonic stem cell
15	chr5:126432200-126433400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr5:126432200-126435000	Enhancers	Fetal Thymus	thymus
17	chr5:126432400-126433200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr5:126432600-126433600	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr5:126432600-126433800	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr5:126432800-126433600	Enhancers	Brain Germinal Matrix	brain
21	chr5:126432800-126434200	Enhancers	HepG2	liver
22	chr5:126433000-126433200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:126433000-126433400	Enhancers	H1 Cell Line	embryonic stem cell

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