Variant report

Variant	rs10193032
Chromosome Location	chr2:74051612-74051613
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr2:74050875-74051729	SK-N-SH	brain:	n/a	n/a
2	RAD21	chr2:74050970-74051658	SK-N-SH	brain:	n/a	n/a
3	CTCF	chr2:74050803-74051908	A549	lung:	n/a	n/a
4	RAD21	chr2:74050929-74051645	A549	lung:	n/a	n/a
5	CTCF	chr2:74051480-74051630	AG10803	skin:	n/a	n/a
6	RAD21	chr2:74050917-74051677	HCT-116	colon:	n/a	n/a
7	SMC3	chr2:74051034-74051683	SK-N-SH	brain:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr2:74040863..74045251-chr2:74049406..74052503,5	K562	blood:
2	chr2:74043930..74046271-chr2:74049022..74051900,2	K562	blood:
3	chr2:74050589..74053188-chr2:74425488..74428809,3	K562	blood:
4	chr2:74048232..74053835-chr2:74054336..74058282,6	MCF-7	breast:
5	chr2:74050746..74051626-chr2:74346995..74347813,2	K562	blood:
6	chr2:74051254..74054251-chr2:74054694..74057544,2	MCF-7	breast:
7	chr2:74040722..74043858-chr2:74049406..74052392,4	K562	blood:
8	chr2:74048023..74052470-chr2:74054588..74058277,4	K562	blood:

No data

Variant related genes	Relation type
STAMBP	TF binding region
ENSG00000257800	Chromatin interaction
ENSG00000065911	Chromatin interaction
ENSG00000124356	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10172044	0.81[ASN][1000 genomes]
rs10203740	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10208995	0.91[ASN][1000 genomes]
rs11126415	1.00[JPT][hapmap]
rs11126416	0.81[CHB][hapmap];0.81[ASN][1000 genomes]
rs11126417	0.83[TSI][hapmap]
rs11892172	0.85[CHB][hapmap];0.85[ASN][1000 genomes]
rs11894953	0.81[CHB][hapmap];0.81[CHD][hapmap];0.83[TSI][hapmap]
rs12619258	1.00[JPT][hapmap]
rs12624267	0.81[CHB][hapmap];0.81[CHD][hapmap];0.88[TSI][hapmap];0.84[ASN][1000 genomes]
rs12713793	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.86[ASN][1000 genomes]
rs12713794	0.85[ASN][1000 genomes]
rs12713795	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12713797	0.81[ASN][1000 genomes]
rs12713798	0.81[CHB][hapmap];0.81[CHD][hapmap];0.83[TSI][hapmap];0.84[ASN][1000 genomes]
rs12992607	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs13003035	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs13006598	0.98[ASN][1000 genomes]
rs13020517	0.80[ASN][1000 genomes]
rs13033744	0.81[CHB][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap];0.80[ASN][1000 genomes]
rs13383097	0.98[ASN][1000 genomes]
rs17009372	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs17350125	1.00[JPT][hapmap]
rs17350188	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.88[ASN][1000 genomes]
rs2116367	0.81[CHB][hapmap];0.85[ASN][1000 genomes]
rs2272051	0.83[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.96[ASN][1000 genomes]
rs2272178	0.91[ASN][1000 genomes]
rs2421559	0.83[CEU][hapmap];0.81[CHB][hapmap];0.80[CHD][hapmap];0.88[TSI][hapmap];0.85[ASN][1000 genomes]
rs2421574	0.87[GIH][hapmap]
rs2421672	1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs2421674	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.86[ASN][1000 genomes]
rs2421675	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2421676	0.81[CHB][hapmap];0.80[CHD][hapmap];0.83[TSI][hapmap];0.81[ASN][1000 genomes]
rs2462127	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs35791379	0.81[ASN][1000 genomes]
rs3813228	0.83[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.96[ASN][1000 genomes]
rs4358149	0.88[ASN][1000 genomes]
rs4852975	0.83[CHD][hapmap]
rs4852976	0.83[CHD][hapmap];1.00[JPT][hapmap]
rs6742619	0.82[CEU][hapmap]
rs7210	1.00[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap];0.86[ASN][1000 genomes]
rs732778	0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7597302	0.92[ASN][1000 genomes]
rs7606947	0.87[GIH][hapmap]
rs891695	0.86[ASN][1000 genomes]
rs891696	0.83[ASN][1000 genomes]
rs9309475	0.81[ASN][1000 genomes]
rs9309476	0.91[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	esv2757806	chr2:73717032-74078592	Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2759060	chr2:73717032-74078592	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv834260	chr2:73906106-74076520	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv2780	chr2:73994168-74057248	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10193032	ALMS1P	cis	Nerve Tibial	GTEx
rs10193032	DUSP11	cis	cerebellum	SCAN
rs10193032	MPHOSPH10	cis	cerebellum	SCAN
rs10193032	CGI-121	cis	multi-tissue	Pritchard
rs10193032	ALMS1	cis	cerebellum	SCAN
rs10193032	TPRKB	Cis_1M	lymphoblastoid	RTeQTL
rs10193032	DUSP11	cis	parietal	SCAN
rs10193032	STAMBP	cis	multi-tissue	Pritchard

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74048800-74054800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr2:74050000-74054800	Weak transcription	Primary B cells from peripheral blood	blood
3	chr2:74050800-74054600	Weak transcription	GM12878-XiMat	blood
4	chr2:74051000-74051800	Enhancers	Adipose Nuclei	Adipose
5	chr2:74051000-74052200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr2:74051400-74052800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr2:74051600-74054600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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