Variant report

Variant	rs11709875
Chromosome Location	chr3:141180511-141180512
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:141179088..141181324-chr3:141593928..141596334,2	K562	blood:
2	chr3:141177718..141181324-chr3:141593928..141596478,3	K562	blood:
3	chr3:141179479..141182374-chr3:141204762..141206399,2	MCF-7	breast:
4	chr3:141178968..141180548-chr3:141278934..141280564,2	K562	blood:
5	chr3:141179908..141182127-chr3:141182376..141185079,2	K562	blood:

Variant related genes	Relation type
ENSG00000155903	Chromatin interaction
ENSG00000069849	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1077181	0.96[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11707656	0.84[AMR][1000 genomes]
rs11708253	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11714208	0.85[CEU][hapmap];0.93[MEX][hapmap]
rs11716776	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11717144	0.92[CEU][hapmap]
rs11717842	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12695734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12695735	0.96[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12695736	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12695740	0.87[CEU][hapmap];0.92[MEX][hapmap]
rs12695741	0.90[CEU][hapmap]
rs12695743	0.84[CEU][hapmap]
rs13059128	0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13072100	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13078872	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13083593	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13084444	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13088429	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13095168	0.92[CEU][hapmap]
rs13098300	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13099945	0.92[CEU][hapmap]
rs1863870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2312194	0.82[AMR][1000 genomes]
rs2312266	1.00[ASN][1000 genomes]
rs34342794	0.81[AMR][1000 genomes]
rs3806647	0.84[AMR][1000 genomes]
rs720663	0.92[CEU][hapmap];0.93[MEX][hapmap]
rs7636914	1.00[GIH][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes]
rs9289629	0.96[CEU][hapmap];0.93[MEX][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9289634	0.92[CEU][hapmap]
rs9808953	0.92[CEU][hapmap]
rs9822575	0.92[CEU][hapmap];0.93[MEX][hapmap]
rs9823528	0.82[AMR][1000 genomes]
rs9830055	0.92[CEU][hapmap]
rs9833121	0.92[CEU][hapmap];0.93[MEX][hapmap]
rs9836050	0.92[CEU][hapmap];0.80[YRI][hapmap]
rs9837202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9838230	0.84[AMR][1000 genomes]
rs9838419	0.82[AMR][1000 genomes]
rs9840697	0.82[AMR][1000 genomes]
rs9849180	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9850416	0.92[CEU][hapmap];0.93[MEX][hapmap]
rs9865971	0.96[CEU][hapmap];0.93[MEX][hapmap]
rs9868956	0.92[CEU][hapmap];0.80[YRI][hapmap];0.82[AMR][1000 genomes]
rs9870749	0.92[CEU][hapmap];0.93[MEX][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829744	chr3:141016749-141189168	Genic enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11709875	ZBTB38	cis	cerebellum	SCAN
rs11709875	ATR	cis	parietal	SCAN
rs11709875	ATP1B3	cis	cerebellum	SCAN
rs11709875	RASA2	cis	cerebellum	SCAN
rs11709875	GK5	cis	parietal	SCAN
rs11709875	RASA2	cis	parietal	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141166600-141181600	Weak transcription	Pancreas	Pancrea
2	chr3:141168600-141181800	Weak transcription	Aorta	Aorta
3	chr3:141174200-141181000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr3:141174200-141182200	Weak transcription	Brain Hippocampus Middle	brain
5	chr3:141174200-141182400	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:141174200-141182400	Weak transcription	Brain Substantia Nigra	brain
7	chr3:141174800-141180800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:141176800-141183600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:141177000-141183800	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr3:141177000-141184000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr3:141177000-141189600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:141178000-141184200	Weak transcription	NHLF	lung
13	chr3:141178000-141188200	Weak transcription	NHDF-Ad	bronchial
14	chr3:141178400-141181000	Weak transcription	HepG2	liver
15	chr3:141179400-141180800	Weak transcription	Primary B cells from peripheral blood	blood
16	chr3:141179400-141181000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr3:141179400-141183800	Weak transcription	NH-A	brain
18	chr3:141179600-141181000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr3:141179600-141182400	Weak transcription	A549	lung
20	chr3:141179600-141183800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:141179600-141184000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:141179600-141184000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr3:141179600-141184000	Weak transcription	Osteobl	bone

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