Variant report

Variant	rs11802812
Chromosome Location	chr1:224803125-224803126
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr1:224803073-224803934	U2OS	brain:	n/a	n/a
2	E2F6	chr1:224803117-224805791	H1-hESC	embryonic stem cell:	n/a	chr1:224803938-224803952 chr1:224803665-224803675 chr1:224804409-224804424 chr1:224805253-224805265

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:224760255..224762194-chr1:224803067..224805853,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-WDR26-1	chr1:224802906-224803129	XLOC_001228
2	lnc-WDR26-1	chr1:224802998-224803129	XLOC_001228
3	lnc-WDR26-1	chr1:224802920-224803129	XLOC_001228
4	lnc-WDR26-1	chr1:224802906-224803149	XLOC_001228

Variant related genes	Relation type
CNIH3	TF binding region
ENSG00000229991	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10799588	0.88[ASN][1000 genomes]
rs11803050	1.00[AMR][1000 genomes]
rs11804994	1.00[AMR][1000 genomes]
rs16849654	1.00[JPT][hapmap]
rs57209437	0.93[ASN][1000 genomes]
rs58565730	0.93[ASN][1000 genomes]
rs59018094	0.80[ASN][1000 genomes]
rs59610983	0.93[ASN][1000 genomes]
rs59643307	0.93[ASN][1000 genomes]
rs61247305	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6657458	0.93[ASN][1000 genomes]
rs6693360	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7534595	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7539939	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7550112	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11802812	CAPN2	cis	lymphoblastoid	seeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224797600-224803200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr1:224797600-224803400	Weak transcription	Psoas Muscle	Psoas
3	chr1:224801000-224803200	Weak transcription	Pancreas	Pancrea
4	chr1:224802000-224803200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:224802800-224803200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:224802800-224803400	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:224802800-224803800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr1:224803000-224803200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
9	chr1:224803000-224803200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
10	chr1:224803000-224803200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
11	chr1:224803000-224803200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:224803000-224803200	Enhancers	NHDF-Ad	bronchial
13	chr1:224803000-224803200	Bivalent/Poised TSS	Osteobl	bone
14	chr1:224803000-224803400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
15	chr1:224803000-224803400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr1:224803000-224803400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
17	chr1:224803000-224803600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
18	chr1:224803000-224803600	Bivalent Enhancer	Fetal Thymus	thymus
19	chr1:224803000-224803800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:224803000-224803800	Flanking Active TSS	Dnd41	blood
21	chr1:224803000-224803800	Flanking Active TSS	NH-A	brain
22	chr1:224803000-224804000	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
23	chr1:224803000-224804000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin

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