Variant report

Variant	rs10171858
Chromosome Location	chr2:31393214-31393215
allele	A/G
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr2:30934379..30935101-chr2:31392582..31393517,4	MCF-7	breast:
2	chr2:30937140..30937644-chr2:31393091..31393610,2	MCF-7	breast:
3	chr2:30938969..30939544-chr2:31392686..31393613,2	MCF-7	breast:
4	chr2:31272032..31272775-chr2:31392833..31393525,2	MCF-7	breast:
5	chr2:31084008..31085526-chr2:31392671..31393659,6	MCF-7	breast:
6	chr2:30934393..30935214-chr2:31392750..31393384,3	MCF-7	breast:
7	chr2:31374189..31375034-chr2:31392805..31393608,2	MCF-7	breast:
8	chr2:31085085..31085843-chr2:31392722..31393572,3	K562	blood:

No data

Extended variants
information (count: 45 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10168043	0.84[ASN][1000 genomes]
rs10172706	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10180369	0.84[ASN][1000 genomes]
rs10184074	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12620887	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12622868	0.97[ASN][1000 genomes]
rs12992405	0.82[CHB][hapmap];0.84[CHD][hapmap];0.80[JPT][hapmap]
rs13421721	0.85[AMR][1000 genomes]
rs1348437	0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1373217	0.85[ASN][1000 genomes]
rs1443708	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1443709	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1443710	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1443712	0.85[ASN][1000 genomes]
rs1443713	0.91[ASN][1000 genomes]
rs1443714	0.85[ASN][1000 genomes]
rs1465972	0.82[CHB][hapmap]
rs2028675	0.82[AMR][1000 genomes]
rs2028677	0.83[AMR][1000 genomes]
rs2044244	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2044245	0.81[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2044246	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap]
rs4592896	0.92[CHB][hapmap]
rs4952051	0.83[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57684646	0.82[AMR][1000 genomes]
rs6720151	0.84[AMR][1000 genomes]
rs6741329	1.00[CEU][hapmap];0.92[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7422120	0.82[CHB][hapmap]
rs7564478	0.82[AMR][1000 genomes]
rs7579175	0.84[AMR][1000 genomes]
rs7599162	0.85[ASN][1000 genomes]
rs7602639	0.84[ASN][1000 genomes]
rs9308916	0.81[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs9308917	0.91[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs961641	0.82[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs961642	0.94[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[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	nsv948552	chr2:31118599-31595424	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv873771	chr2:31363732-31416582	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv873772	chr2:31363732-31417863	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv873773	chr2:31363732-31426449	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv873774	chr2:31363732-31432367	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv873775	chr2:31363732-31439443	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv873776	chr2:31384009-31439443	Enhancers Bivalent Enhancer Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv997652	chr2:31385242-31431588	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv535611	chr2:31385242-31431588	ZNF genes & repeats Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10171858	TCF23	cis	cerebellum	SCAN
rs10171858	EIF2B4	cis	cerebellum	SCAN
rs10171858	CLIP4	cis	parietal	SCAN
rs10171858	Hs.468081	cis	multi-tissue	Pritchard
rs10171858	KRTCAP3	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:31388400-31407000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr2:31391200-31418600	Weak transcription	Gastric	stomach
3	chr2:31393000-31393400	Enhancers	Fetal Heart	heart
4	chr2:31393000-31395200	Enhancers	Primary B cells from peripheral blood	blood

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