Variant report

Variant	rs4725560
Chromosome Location	chr7:139640567-139640568
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	chr7:139639209..139641304-chr7:139657486..139660196,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CLEC2L-4	chr7:139639478-139646946	NONHSAT123657

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1003816	0.85[CHB][hapmap]
rs1034791	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12666944	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1544451	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1557967	0.86[CHB][hapmap];0.80[CHD][hapmap]
rs2008582	0.93[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2014454	0.99[ASN][1000 genomes]
rs2107901	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2158668	0.94[ASN][1000 genomes]
rs2190087	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2284207	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2284208	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2284209	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2284210	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2299894	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4140996	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs42335	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs4629769	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4725563	0.86[CHB][hapmap]
rs4726473	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4726477	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs740148	0.92[ASN][1000 genomes]
rs757759	0.93[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs757760	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs886697	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs917147	0.86[CHB][hapmap];0.81[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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
10	esv3412516	chr7:139640404-139640587	Weak transcription Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4725560	AGK	cis	parietal	SCAN
rs4725560	SLC6A13	trans	brain	seeQTL
rs4725560	SLC13A4	trans	brain	seeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:139615400-139645000	Weak transcription	Primary T cells from cord blood	blood
2	chr7:139618600-139644800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr7:139634000-139656800	Weak transcription	Thymus	Thymus
4	chr7:139634200-139642200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr7:139636800-139645400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr7:139636800-139645400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr7:139637600-139644800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr7:139638200-139645000	Weak transcription	Lung	lung
9	chr7:139638600-139641400	Weak transcription	Primary B cells from peripheral blood	blood
10	chr7:139638600-139645000	Weak transcription	Primary B cells from cord blood	blood
11	chr7:139638600-139645600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr7:139638600-139645600	Weak transcription	Fetal Thymus	thymus
13	chr7:139638800-139640800	Weak transcription	K562	blood
14	chr7:139639400-139641800	Weak transcription	Primary hematopoietic stem cells	blood
15	chr7:139640000-139644800	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr7:139640200-139641000	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr7:139640200-139644200	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr7:139640200-139644800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr7:139640400-139641600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr7:139640400-139644800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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