Variant report

Variant	rs12096552
Chromosome Location	chr1:168463373-168463374
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	chr1:168449934..168452789-chr1:168461978..168463647,2	K562	blood:
2	chr1:168461061..168463419-chr1:168464671..168466571,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000237658	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10918916	1.00[AMR][1000 genomes]
rs10918918	1.00[AMR][1000 genomes]
rs12059095	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12060094	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12061311	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12061688	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12062599	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12064517	1.00[TSI][hapmap];1.00[AMR][1000 genomes]
rs12064716	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12071398	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12071533	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12075383	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12076618	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12078253	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12087491	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12088031	1.00[AMR][1000 genomes]
rs12088109	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12093369	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12095242	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12096533	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12563551	1.00[TSI][hapmap]
rs16860759	1.00[AMR][1000 genomes]
rs28537856	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014626	chr1:168441288-168642731	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv535196	chr1:168441288-168642731	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1011821	chr1:168441488-168642592	Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv535197	chr1:168441488-168642592	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1008852	chr1:168449940-168643905	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv535198	chr1:168449940-168643905	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv1007846	chr1:168449940-168687265	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:168454600-168475200	Weak transcription	Small Intestine	intestine
2	chr1:168455000-168466800	Weak transcription	Ovary	ovary
3	chr1:168455000-168466800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:168457600-168467200	Weak transcription	Fetal Muscle Leg	muscle
5	chr1:168457800-168468600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:168458600-168463600	Enhancers	Colon Smooth Muscle	Colon
7	chr1:168459800-168464200	Enhancers	HepG2	liver
8	chr1:168461000-168463400	Enhancers	Liver	Liver
9	chr1:168461200-168466800	Weak transcription	Stomach Mucosa	stomach
10	chr1:168461400-168464000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr1:168461400-168466600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:168461400-168466800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr1:168461400-168466800	Weak transcription	Fetal Stomach	stomach
14	chr1:168461400-168467000	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr1:168461600-168464400	Weak transcription	Fetal Intestine Small	intestine
16	chr1:168461600-168464600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr1:168461600-168466400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr1:168461600-168466600	Weak transcription	Fetal Lung	lung
19	chr1:168462000-168464400	Weak transcription	Fetal Intestine Large	intestine
20	chr1:168462000-168467000	Weak transcription	Stomach Smooth Muscle	stomach
21	chr1:168462000-168473400	Weak transcription	Pancreas	Pancrea
22	chr1:168462200-168466400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:168462800-168473600	Weak transcription	Psoas Muscle	Psoas

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