Variant report

Variant	rs1557967
Chromosome Location	chr7:139652819-139652820
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1003816	0.82[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs1034791	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs1544451	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs1557968	0.84[CHB][hapmap];0.84[CHD][hapmap];0.84[MEX][hapmap];0.81[ASN][1000 genomes]
rs2107901	0.86[CHB][hapmap];0.80[CHD][hapmap]
rs2190087	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs2284207	0.86[CHB][hapmap];0.80[CHD][hapmap]
rs2284210	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs2299894	0.86[CHB][hapmap];0.80[CHD][hapmap]
rs4140996	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs4629769	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs4725560	0.86[CHB][hapmap];0.80[CHD][hapmap]
rs4725563	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4726473	0.80[CHD][hapmap]
rs4726477	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs6950008	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs757759	0.83[CHD][hapmap]
rs757760	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs8192835	0.92[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs886697	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs917147	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020234	chr7:139377822-139661964	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1032711	chr7:139411404-139684043	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv464732	chr7:139424022-139654256	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv608472	chr7:139424022-139654256	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1018712	chr7:139429703-139658014	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv831156	chr7:139532318-139694326	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1019001	chr7:139558216-139841268	Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv1029099	chr7:139558216-139869148	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
9	nsv889245	chr7:139599229-139657221	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1557967	PPP2R5D	trans	parietal	SCAN
rs1557967	ZC3HAV1	cis	parietal	SCAN
rs1557967	MRPS33	cis	parietal	SCAN
rs1557967	LOC93432	cis	cerebellum	SCAN
rs1557967	OR6V1	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:139634000-139656800	Weak transcription	Thymus	Thymus
2	chr7:139645800-139653000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr7:139646800-139658600	Weak transcription	Duodenum Mucosa	Duodenum
4	chr7:139647000-139654800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr7:139647000-139660600	Weak transcription	K562	blood
6	chr7:139647600-139653200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr7:139648400-139655200	Weak transcription	Spleen	Spleen
8	chr7:139649800-139658400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr7:139650800-139656400	Weak transcription	Lung	lung
10	chr7:139651000-139653400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr7:139651200-139653000	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr7:139651200-139653200	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr7:139651400-139662400	Weak transcription	Pancreas	Pancrea
14	chr7:139651400-139670000	Weak transcription	Gastric	stomach
15	chr7:139652000-139668400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr7:139652200-139653200	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr7:139652200-139691600	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr7:139652600-139653000	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr7:139652600-139653200	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr7:139652600-139653400	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr7:139652800-139668000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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