Variant report

Variant	rs10875883
Chromosome Location	chr12:49285390-49285391
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:49206484..49210724-chr12:49282235..49285491,4	MCF-7	breast:
2	chr12:49208119..49209061-chr12:49284220..49285446,5	K562	blood:
3	chr12:49253798..49263932-chr12:49272568..49285670,39	MCF-7	breast:
4	chr12:49283029..49285571-chr17:56707837..56709739,2	MCF-7	breast:
5	chr12:49243837..49250262-chr12:49279824..49286856,16	MCF-7	breast:
6	chr12:49245591..49248128-chr12:49284158..49286872,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000212195	Chromatin interaction
ENSG00000172602	Chromatin interaction
ENSG00000167535	Chromatin interaction
ENSG00000174243	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1051886	0.83[CHB][hapmap];0.84[CHD][hapmap]
rs1054376	0.80[CHB][hapmap]
rs10747556	0.88[CHD][hapmap]
rs10747557	0.86[CHB][hapmap]
rs10783287	0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10783289	0.83[CHB][hapmap];0.91[CHD][hapmap]
rs10783293	0.83[CHB][hapmap];0.88[CHD][hapmap]
rs10783294	0.83[CHB][hapmap];0.89[CHD][hapmap]
rs10875885	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs10875886	0.83[CHB][hapmap];0.89[CHD][hapmap]
rs10875893	0.83[CHB][hapmap];0.86[CHD][hapmap]
rs10875894	0.83[CHB][hapmap];0.89[CHD][hapmap]
rs10875897	0.89[CHD][hapmap]
rs10875902	0.84[CHD][hapmap]
rs1111662	0.83[CHB][hapmap];0.89[CHD][hapmap]
rs11168773	0.98[ASN][1000 genomes]
rs11168783	0.83[CHB][hapmap];0.89[CHD][hapmap]
rs11168784	0.83[CHB][hapmap]
rs11168785	0.83[CHB][hapmap];0.86[CHD][hapmap]
rs11168790	0.83[CHB][hapmap];0.89[CHD][hapmap]
rs12369505	0.95[CHB][hapmap];0.94[JPT][hapmap];0.97[ASN][1000 genomes]
rs12423542	0.83[CHB][hapmap];0.88[CHD][hapmap]
rs2073480	0.83[CHB][hapmap];0.89[CHD][hapmap]
rs2272311	0.89[CHD][hapmap]
rs2272312	0.82[CHB][hapmap]
rs2293449	0.83[CHB][hapmap]
rs2446984	0.95[GIH][hapmap];0.81[MEX][hapmap]
rs2446985	0.88[ASN][1000 genomes]
rs2446986	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2446987	0.94[ASN][1000 genomes]
rs2446999	0.82[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs2447000	0.97[ASN][1000 genomes]
rs2447001	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2453476	0.93[ASN][1000 genomes]
rs2926801	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2926806	0.83[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2934998	0.82[GIH][hapmap];0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs2934999	0.83[CEU][hapmap]
rs3741627	0.83[CHB][hapmap];0.84[CHD][hapmap]
rs3759146	0.83[CHB][hapmap];0.89[CHD][hapmap]
rs3782353	0.83[CHB][hapmap];0.84[CHD][hapmap]
rs3809147	0.83[CHB][hapmap];0.89[CHD][hapmap]
rs3825182	0.83[CHB][hapmap];0.89[CHD][hapmap]
rs3825184	0.83[CHB][hapmap];0.89[CHD][hapmap]
rs3958875	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4237854	0.83[CHB][hapmap]
rs4433614	0.82[CHB][hapmap]
rs4760600	0.83[CHB][hapmap];0.89[CHD][hapmap]
rs4760647	0.93[ASN][1000 genomes]
rs4760666	0.89[CHD][hapmap]
rs6580696	0.83[CHB][hapmap];0.89[CHD][hapmap]
rs7297958	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs833476	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs833478	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs833479	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs833483	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs833484	0.82[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs833820	0.81[CEU][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];0.87[MEX][hapmap];0.80[AMR][1000 genomes]
rs833821	0.80[AMR][1000 genomes]
rs833822	0.89[CHD][hapmap]
rs833840	0.85[CEU][hapmap];0.82[MEX][hapmap]
rs833843	0.85[CEU][hapmap];0.87[MEX][hapmap]
rs9783452	0.89[CHD][hapmap]
rs9788029	0.87[AMR][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	nsv469373	chr12:49256792-49285390	Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
2	nsv558832	chr12:49256792-49285390	Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
3	nsv832404	chr12:49258560-49458555	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10875883	FKBP11	cis	parietal	SCAN
rs10875883	FKBP11	cis	cerebellum	SCAN
rs10875883	FKBP11	cis	hippocampus	BrainEAC
rs10875883	FKBP11	cis	brain	BrainEAC
rs10875883	SLC48A1	cis	parietal	SCAN
rs10875883	CCDC65	cis	Esophagus Muscularis	GTEx

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49283800-49285400	Enhancers	Fetal Brain Male	brain
2	chr12:49284200-49285600	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr12:49284400-49285400	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr12:49284400-49285400	Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr12:49284400-49285600	Active TSS	Fetal Brain Female	brain
6	chr12:49284600-49285400	Active TSS	Brain Cingulate Gyrus	brain
7	chr12:49284600-49285600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
8	chr12:49284800-49285400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
9	chr12:49285000-49285400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
10	chr12:49285000-49285400	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr12:49285000-49285400	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
12	chr12:49285000-49285400	Flanking Active TSS	Brain Anterior Caudate	brain
13	chr12:49285000-49285400	Flanking Active TSS	Brain Hippocampus Middle	brain
14	chr12:49285000-49285400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr12:49285200-49285400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr12:49285200-49285400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
17	chr12:49285200-49285400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
18	chr12:49285200-49285400	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:49285200-49285400	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
20	chr12:49285200-49285400	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr12:49285200-49285400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr12:49285200-49285400	Active TSS	Brain Germinal Matrix	brain
23	chr12:49285200-49285400	Enhancers	Brain Substantia Nigra	brain
24	chr12:49285200-49285400	Bivalent Enhancer	Small Intestine	intestine
25	chr12:49285200-49285600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr12:49285200-49285600	Enhancers	Brain Angular Gyrus	brain
27	chr12:49285200-49285600	Bivalent Enhancer	A549	lung

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