Variant report

Variant	rs11112465
Chromosome Location	chr12:105717598-105717599
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:105716740..105719219-chr12:105722490..105724843,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000235162	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10507190	1.00[CHB][hapmap]
rs10861371	0.82[MEX][hapmap]
rs10861388	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10861396	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11112461	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11112467	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11112468	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112469	1.00[CHB][hapmap]
rs11112482	1.00[CHB][hapmap]
rs11112499	1.00[CHB][hapmap]
rs11513891	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11519725	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11613789	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12822081	0.82[MEX][hapmap]
rs12822314	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12827086	0.91[EUR][1000 genomes]
rs12828874	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12829692	1.00[CHB][hapmap]
rs17041538	1.00[CHB][hapmap]
rs2163718	0.90[ASN][1000 genomes]
rs35407439	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35561158	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4545651	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6797	1.00[CHB][hapmap]
rs7299225	0.82[MEX][hapmap]
rs7303242	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.93[LWK][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7303307	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7342398	0.90[ASN][1000 genomes]
rs7959385	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7972400	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972982	0.86[AMR][1000 genomes];0.94[EUR][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	nsv899499	chr12:105616297-105722529	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv510589	chr12:105670071-105743755	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv516472	chr12:105712603-105717598	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11112465	KIAA1033	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105712400-105720000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr12:105712600-105717800	Weak transcription	NHLF	lung
3	chr12:105712800-105719000	Weak transcription	NH-A	brain
4	chr12:105713400-105724000	Weak transcription	Pancreas	Pancrea
5	chr12:105713800-105720400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr12:105713800-105723800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr12:105714600-105720200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:105714600-105724000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr12:105715200-105718000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr12:105715600-105717600	Enhancers	Muscle Satellite Cultured Cells	--
11	chr12:105715800-105719000	Enhancers	HSMM	muscle
12	chr12:105715800-105723800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr12:105716000-105723800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr12:105716200-105717600	Weak transcription	Stomach Mucosa	stomach
15	chr12:105716200-105718000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr12:105716200-105720400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr12:105716400-105720400	Weak transcription	A549	lung
18	chr12:105716400-105723800	Weak transcription	HSMMtube	muscle
19	chr12:105716600-105717800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr12:105716600-105720600	Weak transcription	Osteobl	bone
21	chr12:105716600-105723600	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr12:105716600-105723800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr12:105716800-105717800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr12:105716800-105723600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr12:105716800-105723800	Weak transcription	Fetal Intestine Large	intestine
26	chr12:105717000-105717800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr12:105717200-105717600	Active TSS	NHDF-Ad	bronchial
28	chr12:105717200-105718600	Weak transcription	Fetal Intestine Small	intestine
29	chr12:105717200-105720600	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr12:105717400-105717800	Active TSS	GM12878-XiMat	blood
31	chr12:105717400-105718000	Enhancers	HUVEC	blood vessel

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