Variant report

Variant	rs12485578
Chromosome Location	chr3:43117792-43117793
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1072822	0.94[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12233614	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12485530	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12487785	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12497427	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12497602	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1523125	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1523126	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1566422	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17391761	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17470089	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1815070	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1949583	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1949584	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs488069	0.94[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55764298	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55819365	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55945909	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55954171	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs604033	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6796161	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73074962	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460522	chr3:42967597-43175207	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv590149	chr3:42967597-43175207	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43092800-43117800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:43093400-43120200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr3:43096200-43121200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:43100200-43120200	Weak transcription	Brain Angular Gyrus	brain
5	chr3:43101600-43121000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:43102000-43121000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr3:43102800-43118800	Weak transcription	Brain Hippocampus Middle	brain
8	chr3:43103000-43120000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:43103200-43120600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr3:43104800-43120800	Weak transcription	Gastric	stomach
11	chr3:43105000-43118800	Weak transcription	Thymus	Thymus
12	chr3:43105000-43119600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr3:43106400-43119200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:43106400-43120400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:43112200-43121200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:43112800-43120600	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr3:43113000-43120800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr3:43114800-43118400	Weak transcription	Fetal Muscle Leg	muscle
19	chr3:43115000-43120400	Weak transcription	Fetal Intestine Small	intestine
20	chr3:43115200-43118400	Enhancers	Liver	Liver
21	chr3:43115200-43118400	Weak transcription	Brain Anterior Caudate	brain
22	chr3:43115600-43119000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:43115600-43119600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr3:43116000-43120800	Weak transcription	Dnd41	blood
25	chr3:43116000-43121000	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr3:43116000-43121000	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr3:43116200-43119400	Weak transcription	Primary T cells from cord blood	blood
28	chr3:43116400-43118800	Weak transcription	Fetal Stomach	stomach
29	chr3:43116600-43119600	Weak transcription	Lung	lung
30	chr3:43117000-43119600	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr3:43117000-43119800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr3:43117000-43120200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:43117000-43121200	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr3:43117200-43118800	Weak transcription	Fetal Brain Female	brain
35	chr3:43117200-43119000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr3:43117200-43120200	Weak transcription	Fetal Thymus	thymus
37	chr3:43117200-43120800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr3:43117200-43121000	Weak transcription	Right Ventricle	heart
39	chr3:43117400-43118200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:43117400-43118200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr3:43117400-43118200	Enhancers	Right Atrium	heart
42	chr3:43117400-43118400	Enhancers	Ovary	ovary
43	chr3:43117400-43119600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr3:43117400-43121000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr3:43117600-43117800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr3:43117600-43117800	Enhancers	Esophagus	oesophagus
47	chr3:43117600-43119000	Weak transcription	Aorta	Aorta
48	chr3:43117600-43120000	Weak transcription	Left Ventricle	heart
49	chr3:43117600-43120800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr3:43117600-43121000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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