Variant report

Variant	rs11102625
Chromosome Location	chr1:113949453-113949454
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:113948129..113949831-chr1:113997771..113999315,2	MCF-7	breast:
2	chr1:113930552..113936083-chr1:113941902..113950756,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000081026	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10157946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap]
rs10776770	0.92[CEU][hapmap];1.00[GIH][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap]
rs10857997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12118048	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1936930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2359417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4839318	0.83[ASN][1000 genomes]
rs4839319	0.83[ASN][1000 genomes]
rs6661923	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6694861	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7522365	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap]
rs7523404	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7543189	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs7552954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.95[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	nsv427719	chr1:113570229-114078388	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv999873	chr1:113840351-113949453	Enhancers Flanking Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
3	nsv1010110	chr1:113856612-113969417	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases
4	nsv1014757	chr1:113861524-113969417	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11102625	CTTNBP2NL	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113936000-113952400	Weak transcription	Fetal Stomach	stomach
2	chr1:113937600-113963400	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr1:113939800-113953400	Weak transcription	NHDF-Ad	bronchial
4	chr1:113940200-113952200	Weak transcription	HMEC	breast
5	chr1:113940200-113987000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:113940800-113950000	Weak transcription	Fetal Intestine Large	intestine
7	chr1:113940800-113952200	Weak transcription	Hela-S3	cervix
8	chr1:113941800-113952200	Weak transcription	Colon Smooth Muscle	Colon
9	chr1:113944600-113950600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:113944600-113958200	Weak transcription	Small Intestine	intestine
11	chr1:113944800-113950200	Weak transcription	A549	lung
12	chr1:113944800-113952200	Weak transcription	Stomach Mucosa	stomach
13	chr1:113946000-113949600	Weak transcription	Ovary	ovary
14	chr1:113947000-113950400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr1:113947000-113952400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr1:113948000-113953400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:113948000-113969800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:113948400-113950200	Weak transcription	Liver	Liver
19	chr1:113948600-113949600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr1:113948600-113950600	Weak transcription	Fetal Kidney	kidney
21	chr1:113948600-113953400	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr1:113948800-113950600	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr1:113949200-113950800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:113949400-113949800	Enhancers	Aorta	Aorta

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