Variant report

Variant	rs2468802
Chromosome Location	chr11:18225742-18225743
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr11:18225740-18225890	GM12870	blood:	n/a	n/a
2	RAD21	chr11:18225300-18225769	A549	lung:	n/a	n/a
3	RAD21	chr11:18225256-18225788	A549	lung:	n/a	n/a
4	YY1	chr11:18225229-18225743	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr11:18225133-18226229	A549	lung:	n/a	n/a
6	RAD21	chr11:18225129-18225791	SK-N-SH	brain:	n/a	n/a
7	CTCF	chr11:18225116-18225819	SK-N-SH	brain:	n/a	n/a
8	CTCF	chr11:18225720-18225870	HBMEC	blood vessel:	n/a	n/a
9	RAD21	chr11:18225162-18225758	HCT-116	colon:	n/a	n/a
10	RAD21	chr11:18225224-18225754	HepG2	liver:	n/a	n/a
11	RAD21	chr11:18225244-18225829	HCT-116	colon:	n/a	n/a
12	CTCF	chr11:18225241-18225770	HCT-116	colon:	n/a	n/a
13	YY1	chr11:18225229-18225745	H1-hESC	embryonic stem cell:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr11:18192633..18193561-chr11:18225013..18225969,5	MCF-7	breast:
2	chr11:18224870..18226785-chr11:18415110..18417568,3	K562	blood:
3	chr11:18136749..18137777-chr11:18224999..18225996,5	K562	blood:
4	chr11:18137122..18138032-chr11:18224986..18226232,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000189332	TF binding region
ENSG00000134333	Chromatin interaction
ENSG00000166787	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10832903	0.85[MEX][hapmap]
rs11024552	0.85[MEX][hapmap]
rs1915392	0.95[CHB][hapmap];0.80[JPT][hapmap];0.90[ASN][1000 genomes]
rs2168365	0.88[ASN][1000 genomes]
rs2168366	0.88[ASN][1000 genomes]
rs2263408	0.88[ASN][1000 genomes]
rs2445213	0.88[ASN][1000 genomes]
rs2445215	0.88[ASN][1000 genomes]
rs2445217	0.88[ASN][1000 genomes]
rs2445219	0.88[ASN][1000 genomes]
rs2445220	0.88[ASN][1000 genomes]
rs2445221	0.90[ASN][1000 genomes]
rs2445222	0.90[ASN][1000 genomes]
rs2445223	1.00[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.92[YRI][hapmap];0.91[ASN][1000 genomes]
rs2460820	0.88[ASN][1000 genomes]
rs2460822	1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs2460823	1.00[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs2460828	1.00[CHB][hapmap];0.91[JPT][hapmap];0.92[YRI][hapmap];0.90[ASN][1000 genomes]
rs2460829	0.91[ASN][1000 genomes]
rs2460830	1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.91[ASN][1000 genomes]
rs2468780	0.82[ASN][1000 genomes]
rs2468794	0.91[ASN][1000 genomes]
rs2468795	0.91[ASN][1000 genomes]
rs2468796	0.82[ASN][1000 genomes]
rs2468798	0.80[ASN][1000 genomes]
rs2468799	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs2468800	0.91[ASN][1000 genomes]
rs2468801	1.00[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs2468803	1.00[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs2468804	0.90[ASN][1000 genomes]
rs2468805	0.88[ASN][1000 genomes]
rs2468806	0.88[ASN][1000 genomes]
rs2468808	0.88[ASN][1000 genomes]
rs2468809	0.88[ASN][1000 genomes]
rs2468810	0.87[ASN][1000 genomes]
rs2468811	0.88[ASN][1000 genomes]
rs2468812	0.88[ASN][1000 genomes]
rs2516309	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.91[ASN][1000 genomes]
rs7394556	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv428569	chr11:18194030-18350869	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv521662	chr11:18225742-18227151	Weak transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2468802	CALCA	cis	parietal	SCAN
rs2468802	GCHFR	trans	lymphoblastoid	seeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18211200-18225800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr11:18223400-18226000	Weak transcription	Spleen	Spleen

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