Variant report

Variant	rs2299657
Chromosome Location	chr12:2165956-2165957
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:2165569..2167422-chr12:2392867..2394744,2	MCF-7	breast:

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs10848607	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948480	chr12:1776217-2284333	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv898598	chr12:1939252-2215448	Strong transcription Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv1040370	chr12:2021395-2671017	Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv948400	chr12:2022411-2601363	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv521838	chr12:2060580-2299680	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1035885	chr12:2077660-2310157	Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv541350	chr12:2077660-2310157	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1038722	chr12:2085035-2308205	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv541351	chr12:2085035-2308205	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv898601	chr12:2124955-2215448	Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv826182	chr12:2136395-2208074	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv826183	chr12:2147469-2257818	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv898602	chr12:2149786-2223740	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv557007	chr12:2162369-2165956	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2299657	RAD51AP1	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:2160800-2166200	Active TSS	Brain Angular Gyrus	brain
2	chr12:2161000-2167000	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr12:2161400-2166200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr12:2162800-2178600	Enhancers	Fetal Heart	heart
5	chr12:2163600-2168600	Flanking Active TSS	Stomach Smooth Muscle	stomach
6	chr12:2164200-2167200	Weak transcription	Brain Substantia Nigra	brain
7	chr12:2164400-2167600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr12:2164400-2173400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr12:2164600-2166400	Weak transcription	Ovary	ovary
10	chr12:2164800-2166400	Bivalent Enhancer	Fetal Brain Male	brain
11	chr12:2165000-2166800	Enhancers	NHDF-Ad	bronchial
12	chr12:2165000-2178000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr12:2165200-2166200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr12:2165400-2166000	Bivalent Enhancer	Fetal Lung	lung
15	chr12:2165400-2166400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr12:2165400-2166400	Weak transcription	Pancreas	Pancrea
17	chr12:2165400-2166600	Weak transcription	Aorta	Aorta
18	chr12:2165400-2166600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr12:2165400-2172800	Weak transcription	Osteobl	bone
20	chr12:2165400-2173000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr12:2165600-2166000	Bivalent Enhancer	Brain Germinal Matrix	brain
22	chr12:2165600-2166000	Bivalent Enhancer	Fetal Brain Female	brain
23	chr12:2165600-2166000	Weak transcription	Right Atrium	heart
24	chr12:2165600-2166200	Weak transcription	Brain Hippocampus Middle	brain
25	chr12:2165600-2166400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr12:2165600-2166400	Weak transcription	Brain Anterior Caudate	brain
27	chr12:2165600-2166400	Weak transcription	Gastric	stomach
28	chr12:2165600-2167600	Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr12:2165800-2166200	Enhancers	Pancreatic Islets	Pancreatic Islet
30	chr12:2165800-2166200	Weak transcription	Left Ventricle	heart
31	chr12:2165800-2166200	Weak transcription	Spleen	Spleen
32	chr12:2165800-2166400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr12:2165800-2166400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr12:2165800-2166400	Enhancers	Rectal Smooth Muscle	rectum
35	chr12:2165800-2166600	Flanking Active TSS	Colon Smooth Muscle	Colon
36	chr12:2165800-2166600	Weak transcription	Right Ventricle	heart
37	chr12:2165800-2166800	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr12:2165800-2172800	Weak transcription	NHLF	lung

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