Variant report

Variant	rs2299660
Chromosome Location	chr12:2223883-2223884
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10848617	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1558321	0.85[CHB][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1558322	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2238027	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2238029	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2238033	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2238034	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs2238036	0.85[JPT][hapmap]
rs2239130	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2239131	0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2239133	0.91[EUR][1000 genomes]
rs2239134	0.88[EUR][1000 genomes]
rs2239135	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2247833	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs2283281	0.80[AMR][1000 genomes]
rs2283282	0.80[AMR][1000 genomes]
rs2299661	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2299662	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2299663	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2299664	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4126711	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4765897	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4765898	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs7298821	0.81[JPT][hapmap]
rs758723	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs874924	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs881303	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	nsv898603	chr12:2208390-2268143	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv1053798	chr12:2214047-2253488	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv557033	chr12:2215448-2252924	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv1041740	chr12:2218997-2259643	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:2208400-2226600	Weak transcription	Brain Angular Gyrus	brain
2	chr12:2211800-2229000	Weak transcription	Osteobl	bone
3	chr12:2216800-2224400	Enhancers	Left Ventricle	heart
4	chr12:2217200-2224200	Enhancers	Right Ventricle	heart
5	chr12:2217800-2229600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:2219000-2234000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr12:2220400-2224600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr12:2220400-2224600	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr12:2220400-2228400	Weak transcription	NHDF-Ad	bronchial
10	chr12:2220600-2224600	Weak transcription	Fetal Brain Female	brain
11	chr12:2220600-2228400	Weak transcription	Ovary	ovary
12	chr12:2220800-2235400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr12:2221000-2226200	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr12:2221000-2229000	Weak transcription	Brain Germinal Matrix	brain
15	chr12:2221200-2224600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr12:2221200-2228200	Weak transcription	Fetal Muscle Leg	muscle
17	chr12:2221400-2225000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr12:2221600-2227400	Weak transcription	Fetal Lung	lung
19	chr12:2221800-2229600	Weak transcription	Fetal Brain Male	brain
20	chr12:2222000-2226600	Weak transcription	Fetal Intestine Small	intestine
21	chr12:2222000-2231200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr12:2222000-2235400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr12:2222200-2226200	Weak transcription	Brain Hippocampus Middle	brain
24	chr12:2222400-2239000	Weak transcription	Brain Anterior Caudate	brain
25	chr12:2222600-2224400	Weak transcription	Colon Smooth Muscle	Colon
26	chr12:2222800-2236000	Weak transcription	Lung	lung
27	chr12:2223000-2226800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr12:2223000-2229000	Weak transcription	Esophagus	oesophagus
29	chr12:2223200-2250200	Weak transcription	Brain Substantia Nigra	brain
30	chr12:2223400-2224200	Weak transcription	Stomach Smooth Muscle	stomach
31	chr12:2223400-2224400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr12:2223400-2225000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr12:2223400-2226800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr12:2223400-2228400	Weak transcription	NHLF	lung
35	chr12:2223400-2229600	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr12:2223400-2234000	Weak transcription	Spleen	Spleen
37	chr12:2223600-2224600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr12:2223600-2224600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr12:2223600-2226800	Weak transcription	Fetal Heart	heart
40	chr12:2223600-2227000	Weak transcription	Right Atrium	heart
41	chr12:2223600-2227600	Weak transcription	Aorta	Aorta
42	chr12:2223600-2238200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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