Variant report

Variant	rs10879259
Chromosome Location	chr12:41222390-41222391
allele	A/G
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:20)

rs_ID	r²[population]
rs10784898	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10784901	0.81[EUR][1000 genomes]
rs10879339	0.83[EUR][1000 genomes]
rs10879340	0.83[EUR][1000 genomes]
rs11178530	0.80[ASN][1000 genomes]
rs11178540	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11178967	0.83[EUR][1000 genomes]
rs11178979	0.93[JPT][hapmap]
rs1126373	0.84[CEU][hapmap];0.82[CHB][hapmap];0.81[MEX][hapmap];0.81[ASN][1000 genomes]
rs1584096	0.82[EUR][1000 genomes]
rs1822599	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1854481	0.82[ASN][1000 genomes]
rs1854482	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2772461	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4360771	0.81[ASN][1000 genomes]
rs4768312	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7300719	0.80[EUR][1000 genomes]
rs7967262	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs913831	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs932908	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427909	chr12:41054306-41322257	Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv832379	chr12:41054440-41232749	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv832380	chr12:41132306-41323961	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	esv3435443	chr12:41206734-41222972	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41214000-41223200	Weak transcription	NHEK	skin
2	chr12:41219400-41223400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr12:41220000-41223400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr12:41220200-41222800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:41220600-41223400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr12:41221400-41222400	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
7	chr12:41221400-41222400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
8	chr12:41221400-41222600	Enhancers	H1 Cell Line	embryonic stem cell
9	chr12:41221400-41222600	Enhancers	H9 Cell Line	embryonic stem cell
10	chr12:41221400-41222600	Active TSS	Brain Angular Gyrus	brain
11	chr12:41221400-41222600	Active TSS	Fetal Brain Male	brain
12	chr12:41221400-41222800	Active TSS	Brain Substantia Nigra	brain
13	chr12:41221400-41224000	Active TSS	Brain Cingulate Gyrus	brain
14	chr12:41221400-41224000	Active TSS	Brain Inferior Temporal Lobe	brain
15	chr12:41221400-41224000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
16	chr12:41221600-41222400	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr12:41221600-41222600	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr12:41221600-41222600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr12:41221600-41222600	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr12:41221600-41222800	Flanking Active TSS	A549	lung
21	chr12:41221600-41224000	Enhancers	HMEC	breast
22	chr12:41221800-41222400	Flanking Active TSS	Fetal Brain Female	brain
23	chr12:41221800-41224600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr12:41222000-41222800	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr12:41222000-41222800	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr12:41222200-41222600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
27	chr12:41222200-41222600	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr12:41222200-41222600	Flanking Active TSS	Brain Anterior Caudate	brain
29	chr12:41222200-41222600	Enhancers	Brain Germinal Matrix	brain
30	chr12:41222200-41223000	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr12:41222200-41223000	Enhancers	iPS-18 Cell Line	embryonic stem cell

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