Variant report

Variant	rs12300038
Chromosome Location	chr12:83250063-83250064
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10466960	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10506884	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11115457	0.93[ASW][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11115458	1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11115459	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12304267	0.89[ASN][1000 genomes]
rs12317660	0.89[ASN][1000 genomes]
rs17010056	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs17010066	0.88[JPT][hapmap]
rs17010069	0.88[CEU][hapmap];0.88[JPT][hapmap];0.80[EUR][1000 genomes]
rs1703105	0.88[JPT][hapmap]
rs1703107	0.87[ASN][1000 genomes]
rs6539694	1.00[JPT][hapmap]
rs6539695	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7137977	0.95[ASN][1000 genomes]
rs7301204	0.95[ASN][1000 genomes]
rs7304237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7313758	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs73358290	0.80[ASN][1000 genomes]
rs7979960	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9651971	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053093	chr12:82645292-83287809	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv541551	chr12:82645292-83287809	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv427917	chr12:82917031-83279712	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv521849	chr12:83013783-83991479	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv469490	chr12:83089431-83507269	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv559542	chr12:83089431-83507269	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	esv2758315	chr12:83101045-83357621	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv2759911	chr12:83101045-83357621	Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv430520	chr12:83166956-83271602	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
10	nsv437765	chr12:83230454-83271933	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	n/a
11	nsv832472	chr12:83248283-83419753	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:83196400-83250800	Weak transcription	Fetal Muscle Leg	muscle
2	chr12:83206600-83255200	Weak transcription	Fetal Muscle Trunk	muscle
3	chr12:83212400-83257000	Weak transcription	Gastric	stomach
4	chr12:83214200-83250800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:83229600-83252000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr12:83236000-83250800	Weak transcription	Fetal Lung	lung
7	chr12:83236000-83264000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr12:83236200-83253200	Weak transcription	Fetal Brain Male	brain
9	chr12:83240000-83250800	Weak transcription	Fetal Stomach	stomach
10	chr12:83242200-83289800	Weak transcription	Stomach Mucosa	stomach
11	chr12:83244400-83250800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:83244400-83251200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr12:83244400-83252000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr12:83246400-83253600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr12:83246800-83256000	Weak transcription	Brain Germinal Matrix	brain
16	chr12:83248600-83255800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr12:83249000-83250400	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr12:83249000-83250800	Weak transcription	Fetal Intestine Small	intestine
19	chr12:83249000-83251200	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr12:83249000-83251400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr12:83249000-83252200	Enhancers	Brain Substantia Nigra	brain
22	chr12:83249200-83250600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:83249200-83250600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr12:83249200-83250800	Enhancers	Brain Anterior Caudate	brain
25	chr12:83249200-83256000	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr12:83249400-83250800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr12:83249400-83250800	Enhancers	Brain Cingulate Gyrus	brain
28	chr12:83249400-83256800	Weak transcription	Primary hematopoietic stem cells	blood
29	chr12:83249400-83261000	Weak transcription	Fetal Heart	heart
30	chr12:83249600-83250200	Enhancers	Monocytes-CD14+_RO01746	blood
31	chr12:83249600-83251400	Enhancers	Brain Angular Gyrus	brain
32	chr12:83249600-83251800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr12:83249600-83254000	Weak transcription	Colon Smooth Muscle	Colon
34	chr12:83249600-83261200	Weak transcription	Rectal Smooth Muscle	rectum
35	chr12:83249800-83250800	Enhancers	Brain Hippocampus Middle	brain
36	chr12:83249800-83256000	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr12:83250000-83250600	Weak transcription	Duodenum Mucosa	Duodenum
38	chr12:83250000-83250800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr12:83250000-83251400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr12:83250000-83252200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr12:83250000-83264600	Weak transcription	Duodenum Smooth Muscle	Duodenum

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