Variant report

Variant	rs12424245
Chromosome Location	chr12:2322513-2322514
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1006737	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10459125	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs10744559	0.83[CEU][hapmap]
rs10744560	1.00[JPT][hapmap]
rs10774030	0.83[CEU][hapmap]
rs10774032	0.80[EUR][1000 genomes]
rs10774033	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs10774034	1.00[CHB][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10774035	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10774036	1.00[JPT][hapmap]
rs10848627	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs10848628	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs10848629	0.87[CEU][hapmap]
rs10848631	0.81[EUR][1000 genomes]
rs10848632	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs10848633	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs10848634	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs10848635	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs10848636	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs10848637	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs10848642	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11062145	0.83[CEU][hapmap]
rs11062156	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs11062157	0.82[AMR][1000 genomes]
rs11062159	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11062161	1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11062162	0.85[CHB][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11062166	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11062170	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1108073	1.00[CHB][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1108074	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1108075	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1108221	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1108222	0.95[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12315711	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2098013	0.80[EUR][1000 genomes]
rs2159100	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2190771	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2238046	0.83[CEU][hapmap]
rs2238048	0.82[CEU][hapmap]
rs2238049	0.81[CEU][hapmap]
rs2238050	0.87[CEU][hapmap]
rs2238052	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs2238053	0.87[CEU][hapmap];0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2238054	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs2239018	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs2239019	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs2239020	0.81[EUR][1000 genomes]
rs2239021	0.81[EUR][1000 genomes]
rs2239022	0.81[EUR][1000 genomes]
rs2239023	0.81[EUR][1000 genomes]
rs2239024	0.81[EUR][1000 genomes]
rs2239025	0.81[EUR][1000 genomes]
rs2239026	0.81[EUR][1000 genomes]
rs2239027	0.81[EUR][1000 genomes]
rs2283287	0.82[CEU][hapmap]
rs2283288	0.83[CEU][hapmap]
rs3922316	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4765669	0.81[EUR][1000 genomes]
rs4765670	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs4765902	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs4765904	0.95[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4765905	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7133502	0.80[EUR][1000 genomes]
rs758170	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs758171	0.83[CEU][hapmap]
rs758172	0.81[EUR][1000 genomes]
rs758173	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs758174	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs769087	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7957545	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs7965923	0.82[ASN][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	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
2	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
3	nsv898605	chr12:2252924-2327944	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:2294000-2325200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr12:2301400-2328400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr12:2305200-2322600	Weak transcription	Spleen	Spleen
4	chr12:2308400-2322600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr12:2312800-2323000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr12:2314200-2325000	Enhancers	Right Ventricle	heart
7	chr12:2314600-2322800	Weak transcription	Brain Angular Gyrus	brain
8	chr12:2317000-2324200	Enhancers	Fetal Brain Male	brain
9	chr12:2320400-2335800	Weak transcription	NHLF	lung
10	chr12:2320600-2328000	Weak transcription	Aorta	Aorta
11	chr12:2320800-2331400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr12:2321200-2322600	Enhancers	Fetal Heart	heart
13	chr12:2321400-2325800	Enhancers	Rectal Smooth Muscle	rectum
14	chr12:2321600-2323600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr12:2321600-2324800	Enhancers	Colon Smooth Muscle	Colon
16	chr12:2321600-2325000	Weak transcription	NHDF-Ad	bronchial
17	chr12:2321800-2322800	Enhancers	Brain Anterior Caudate	brain
18	chr12:2321800-2322800	Enhancers	Brain Hippocampus Middle	brain
19	chr12:2321800-2323400	Enhancers	Fetal Stomach	stomach
20	chr12:2321800-2326200	Enhancers	Left Ventricle	heart
21	chr12:2322000-2322800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr12:2322000-2323200	Enhancers	Ovary	ovary
23	chr12:2322000-2323400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr12:2322000-2323400	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr12:2322000-2323400	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr12:2322000-2323400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr12:2322000-2323400	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr12:2322000-2323400	Enhancers	Fetal Kidney	kidney
29	chr12:2322000-2323400	Enhancers	Stomach Smooth Muscle	stomach
30	chr12:2322000-2323800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr12:2322000-2324000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr12:2322200-2322800	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr12:2322200-2323000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr12:2322200-2323000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr12:2322200-2323000	Enhancers	Placenta	Placenta
36	chr12:2322200-2323400	Enhancers	Fetal Intestine Small	intestine
37	chr12:2322200-2323400	Enhancers	Right Atrium	heart
38	chr12:2322200-2323600	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr12:2322200-2323600	Enhancers	Fetal Muscle Trunk	muscle
40	chr12:2322200-2323600	Enhancers	Fetal Muscle Leg	muscle
41	chr12:2322200-2323800	Enhancers	Brain Cingulate Gyrus	brain
42	chr12:2322400-2322600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr12:2322400-2323000	Flanking Active TSS	Fetal Brain Female	brain
44	chr12:2322400-2323200	Enhancers	H1 Cell Line	embryonic stem cell
45	chr12:2322400-2323200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr12:2322400-2323200	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr12:2322400-2323200	Enhancers	Fetal Thymus	thymus
48	chr12:2322400-2323400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr12:2322400-2323400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr12:2322400-2323400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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