Variant report

Variant	rs3131554
Chromosome Location	chr1:186452071-186452072
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:186451484..186452471-chr1:186775451..186776233,2	MCF-7	breast:
2	chr1:186451634..186452411-chr1:186954687..186955318,2	MCF-7	breast:
3	chr1:186451532..186452512-chr1:186651563..186652631,6	MCF-7	breast:
4	chr1:186451494..186452439-chr1:186955128..186955670,2	K562	blood:
5	chr1:186451636..186452892-chr1:186574338..186575805,5	MCF-7	breast:
6	chr1:186451575..186452285-chr1:186731133..186732059,2	MCF-7	breast:
7	chr1:186451676..186452264-chr1:186649134..186649775,2	MCF-7	breast:
8	chr1:186451520..186452510-chr1:186775360..186775901,2	MCF-7	breast:
9	chr1:186451542..186452284-chr1:186651474..186652178,3	MCF-7	breast:
10	chr1:186451467..186452331-chr1:186574622..186575436,4	MCF-7	breast:
11	chr1:186373386..186374034-chr1:186451869..186452455,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000273129	Chromatin interaction
ENSG00000073756	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10494583	0.82[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs10494584	0.82[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs10911902	0.89[CEU][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs12120448	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12124257	1.00[ASW][hapmap]
rs12131484	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12133471	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12137128	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16825150	0.82[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs16825185	0.82[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs16825243	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2272412	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2297226	0.82[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs3119331	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3131556	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3736597	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3753565	0.82[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs3766702	0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap]
rs3766703	0.82[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs3766704	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3766707	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3820181	0.82[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs3820182	0.82[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs55658718	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55660734	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61810323	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425028	0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs6658482	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6664763	0.82[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs6666680	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6678193	0.80[ASN][1000 genomes]
rs6689129	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7514615	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7515126	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7525634	0.80[ASN][1000 genomes]
rs7556543	0.90[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004481	chr1:186095854-186750968	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv535223	chr1:186095854-186750968	Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv1012164	chr1:186323867-186565995	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	esv2762201	chr1:186323879-186566007	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats 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	34 gene(s)	inside rSNPs	diseases
5	nsv527758	chr1:186452071-186456977	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3131554	C1orf27	cis	cerebellum	SCAN
rs3131554	CACNA1E	cis	cerebellum	SCAN
rs3131554	OCLM	cis	parietal	SCAN
rs3131554	KIAA1614	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186451000-186455800	Weak transcription	Osteobl	bone
2	chr1:186451600-186452600	Enhancers	Hela-S3	cervix
3	chr1:186451600-186453200	Enhancers	HUVEC	blood vessel
4	chr1:186451800-186452200	Enhancers	Muscle Satellite Cultured Cells	--
5	chr1:186451800-186452400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr1:186451800-186452400	Enhancers	NHEK	skin
7	chr1:186451800-186452800	Enhancers	A549	lung
8	chr1:186452000-186452400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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