Variant report

Variant	rs4141075
Chromosome Location	chr7:124410577-124410578
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:124405542..124407199-chr7:124408362..124410580,2	MCF-7	breast:
2	chr7:124401538..124403710-chr7:124408710..124411016,2	K562	blood:
3	chr7:124408284..124411028-chr7:124413080..124414599,2	K562	blood:

Variant related genes	Relation type
ENSG00000170775	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1008290	0.84[ASN][1000 genomes]
rs10230948	0.89[ASN][1000 genomes]
rs10234698	0.90[ASN][1000 genomes]
rs10241745	0.89[ASN][1000 genomes]
rs10256073	0.81[CHB][hapmap]
rs10268290	0.85[ASN][1000 genomes]
rs10280030	0.89[ASN][1000 genomes]
rs1034794	0.89[ASN][1000 genomes]
rs1034795	0.89[ASN][1000 genomes]
rs11767519	0.93[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap]
rs11768553	0.93[CHB][hapmap];0.92[JPT][hapmap]
rs11770818	0.93[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap]
rs11772420	0.93[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs12532038	0.93[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs12534967	0.89[ASN][1000 genomes]
rs12537983	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs12539481	0.93[CHB][hapmap];0.92[JPT][hapmap]
rs12706625	0.82[CEU][hapmap];0.93[CHB][hapmap];0.83[CHD][hapmap];0.92[JPT][hapmap]
rs12706627	0.93[CHB][hapmap];0.92[JPT][hapmap]
rs13222197	0.80[ASN][1000 genomes]
rs1541417	0.89[ASN][1000 genomes]
rs17147465	0.90[ASN][1000 genomes]
rs17147723	0.81[CHB][hapmap]
rs2101100	0.93[CHB][hapmap];0.92[JPT][hapmap]
rs2158676	0.84[ASN][1000 genomes]
rs2291207	0.93[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap]
rs2299904	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs2402754	0.89[ASN][1000 genomes]
rs28730874	0.97[ASN][1000 genomes]
rs2896357	0.84[ASN][1000 genomes]
rs34326887	0.86[ASN][1000 genomes]
rs35550222	0.86[ASN][1000 genomes]
rs4141073	0.89[ASN][1000 genomes]
rs4360236	0.93[CHB][hapmap];0.82[CHD][hapmap];0.92[JPT][hapmap]
rs4501522	0.93[CHB][hapmap];0.92[JPT][hapmap]
rs4577901	0.84[ASN][1000 genomes]
rs4639456	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4728005	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4728007	0.89[ASN][1000 genomes]
rs4731210	0.91[ASN][1000 genomes]
rs62480274	0.80[ASN][1000 genomes]
rs6466951	0.85[ASN][1000 genomes]
rs6943703	0.87[ASN][1000 genomes]
rs6943797	0.89[ASN][1000 genomes]
rs6946962	0.81[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap]
rs6963885	0.89[ASN][1000 genomes]
rs6968018	0.89[ASN][1000 genomes]
rs6977430	0.84[ASN][1000 genomes]
rs716991	0.91[ASN][1000 genomes]
rs717241	0.85[ASN][1000 genomes]
rs73443822	0.83[ASN][1000 genomes]
rs7782296	0.84[ASN][1000 genomes]
rs7782351	0.82[ASN][1000 genomes]
rs7784168	0.86[CEU][hapmap];0.93[CHB][hapmap];0.83[CHD][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs7787804	0.87[CHB][hapmap];0.84[CHD][hapmap];0.89[ASN][1000 genomes]
rs7794637	0.93[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs7795610	0.89[ASN][1000 genomes]
rs7796751	0.89[ASN][1000 genomes]
rs9641745	0.84[ASN][1000 genomes]
rs9656320	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429809	chr7:123937674-124835925	Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
2	esv3446198	chr7:124358002-124586856	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4141075	VIM	trans	lymphoblastoid	seeQTL
rs4141075	RNF34	trans	lymphoblastoid	seeQTL
rs4141075	OGFRL1	trans	lymphoblastoid	seeQTL
rs4141075	HPCAL1	trans	lymphoblastoid	seeQTL

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:124406200-124410800	Weak transcription	HUVEC	blood vessel
2	chr7:124406800-124410600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr7:124406800-124410600	Weak transcription	Brain Angular Gyrus	brain
4	chr7:124406800-124410600	Weak transcription	Brain Substantia Nigra	brain
5	chr7:124406800-124410800	Weak transcription	Brain Anterior Caudate	brain
6	chr7:124406800-124411000	Weak transcription	Brain Cingulate Gyrus	brain
7	chr7:124406800-124412000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr7:124410000-124411200	Enhancers	Brain Hippocampus Middle	brain
9	chr7:124410400-124410800	Enhancers	HUES64 Cell Line	embryonic stem cell

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