Variant report

Variant	rs2896357
Chromosome Location	chr7:124379865-124379866
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1008290	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11767519	0.93[CHB][hapmap]
rs11768553	0.93[CHB][hapmap];0.85[JPT][hapmap]
rs11770818	0.93[CHB][hapmap];0.85[JPT][hapmap]
rs11772420	0.93[CHB][hapmap];0.85[JPT][hapmap]
rs12155299	0.93[ASN][1000 genomes]
rs12532038	0.93[CHB][hapmap];0.85[JPT][hapmap]
rs12537983	0.92[CHB][hapmap]
rs12539481	0.93[CHB][hapmap];0.85[JPT][hapmap]
rs12706625	0.93[CHB][hapmap];0.85[JPT][hapmap]
rs12706627	0.93[CHB][hapmap];0.84[JPT][hapmap]
rs17147723	0.81[CHB][hapmap]
rs2101100	0.93[CHB][hapmap];0.85[JPT][hapmap]
rs2158676	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2291207	0.93[CHB][hapmap];0.85[JPT][hapmap]
rs2299904	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs28730874	0.82[ASN][1000 genomes]
rs4141075	1.00[CHB][hapmap];0.81[CHD][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs4360236	0.93[CHB][hapmap];0.85[JPT][hapmap]
rs4501522	0.93[CHB][hapmap];0.85[JPT][hapmap]
rs4577901	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4639456	1.00[CHB][hapmap];0.81[CHD][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs4728005	1.00[CHB][hapmap];0.86[CHD][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs6946962	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs6977430	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs717241	0.99[ASN][1000 genomes]
rs73443822	0.96[ASN][1000 genomes]
rs7778121	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7784168	0.93[CHB][hapmap];0.84[JPT][hapmap]
rs7787804	0.87[CHB][hapmap]
rs7794637	0.93[CHB][hapmap]
rs9641745	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[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	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	nsv1027091	chr7:124311742-124388908	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	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
4	esv1802433	chr7:124365503-124385252	Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2896357	HNF1B	trans	lymphoblastoid	seeQTL
rs2896357	RGS17	trans	lymphoblastoid	seeQTL
rs2896357	EPS8	trans	lymphoblastoid	seeQTL
rs2896357	C5orf13	trans	lymphoblastoid	seeQTL
rs2896357	OGFRL1	trans	lymphoblastoid	seeQTL
rs2896357	VIM	trans	lymphoblastoid	seeQTL
rs2896357	RCAN1	trans	lymphoblastoid	seeQTL
rs2896357	C1orf106	trans	lymphoblastoid	seeQTL
rs2896357	PLCL2	trans	lymphoblastoid	seeQTL
rs2896357	C11orf9	trans	lymphoblastoid	seeQTL
rs2896357	SASH1	trans	lymphoblastoid	seeQTL
rs2896357	MYO6	trans	lymphoblastoid	seeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:124376800-124389400	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr7:124378000-124380600	Enhancers	Brain Substantia Nigra	brain
3	chr7:124378600-124384200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr7:124378600-124396600	Weak transcription	Fetal Lung	lung
5	chr7:124378800-124382400	Weak transcription	Brain Angular Gyrus	brain
6	chr7:124379000-124380000	Weak transcription	Brain Hippocampus Middle	brain
7	chr7:124379000-124382400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr7:124379000-124382600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr7:124379000-124386600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr7:124379600-124385400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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