Variant report

Variant	rs895953
Chromosome Location	chr12:122249048-122249049
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:122127725..122130645-chr12:122248269..122249908,2	MCF-7	breast:
2	chr12:122247207..122249195-chr12:122326533..122328420,2	K562	blood:
3	chr12:122063951..122065995-chr12:122247788..122250462,2	K562	blood:
4	chr12:122231599..122234135-chr12:122248993..122250611,25	K562	blood:
5	chr12:122248261..122250209-chr12:122294921..122296853,2	MCF-7	breast:
6	chr12:122148543..122152154-chr12:122247522..122251412,4	MCF-7	breast:
7	chr12:122248304..122251064-chr12:132568953..132570962,2	MCF-7	breast:
8	chr12:122248762..122251835-chr12:122331420..122334118,3	MCF-7	breast:
9	chr12:122248656..122250378-chr12:122275889..122277499,2	K562	blood:
10	chr12:122219428..122221615-chr12:122247331..122249175,2	K562	blood:
11	chr12:122202998..122205490-chr12:122248231..122250128,2	K562	blood:
12	chr12:122247695..122252163-chr12:122325172..122328033,7	K562	blood:
13	chr12:122248283..122252969-chr12:122325592..122328736,7	MCF-7	breast:
14	chr12:122231820..122233222-chr12:122248899..122249520,4	MCF-7	breast:
15	chr12:120729818..120731411-chr12:122247604..122250047,3	MCF-7	breast:
16	chr12:122138274..122140885-chr12:122248656..122250859,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000139725	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000110801	Chromatin interaction
ENSG00000188735	Chromatin interaction
ENSG00000256950	Chromatin interaction
ENSG00000158104	Chromatin interaction
ENSG00000182500	Chromatin interaction
ENSG00000185684	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1004390	0.92[EUR][1000 genomes]
rs11043202	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11043203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11043207	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs1168663	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1168664	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1168665	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1168666	1.00[CEU][hapmap];0.80[GIH][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1168668	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1168669	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1168671	1.00[CEU][hapmap];0.80[GIH][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1168672	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1168673	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12307227	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12823194	0.85[EUR][1000 genomes]
rs1667578	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1667579	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1795965	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1795966	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2019561	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2019562	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2122266	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2707066	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2707067	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs712852	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7957564	0.92[EUR][1000 genomes]
rs7974348	1.00[CEU][hapmap];0.80[GIH][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs895951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs895952	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs895954	1.00[CEU][hapmap];0.80[GIH][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs895957	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs921286	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs921287	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs921288	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs930665	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv899566	chr12:122167095-122265106	Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
3	nsv899567	chr12:122203680-122281575	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
4	nsv984477	chr12:122226309-122271532	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
5	nsv911	chr12:122234524-122279425	Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
6	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs895953	LOC338799	cis	cerebellum	SCAN
rs895953	MPHOSPH9	cis	cerebellum	SCAN
rs895953	SBNO1	cis	parietal	SCAN
rs895953	LOC338799	cis	parietal	SCAN
rs895953	LOC338799	cis	multi-tissue	Pritchard
rs895953	CCDC60	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122243800-122251600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr12:122244400-122249200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:122244800-122249200	Weak transcription	Psoas Muscle	Psoas
4	chr12:122245400-122249600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr12:122247200-122251400	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr12:122247400-122249200	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:122247400-122249400	Genic enhancers	Spleen	Spleen
8	chr12:122247600-122249400	Genic enhancers	Gastric	stomach
9	chr12:122247800-122252000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr12:122248000-122249400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr12:122248200-122249200	Genic enhancers	Primary monocytes fromperipheralblood	blood
12	chr12:122248200-122249200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr12:122248200-122249200	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr12:122248200-122249200	Genic enhancers	Esophagus	oesophagus
15	chr12:122248200-122249200	Genic enhancers	Fetal Muscle Leg	muscle
16	chr12:122248200-122249200	Genic enhancers	Right Ventricle	heart
17	chr12:122248200-122249400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr12:122248200-122249400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr12:122248200-122249400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr12:122248200-122249400	Genic enhancers	Fetal Muscle Trunk	muscle
21	chr12:122248200-122249400	Enhancers	Right Atrium	heart
22	chr12:122248200-122249600	Genic enhancers	Fetal Stomach	stomach
23	chr12:122248200-122250800	Transcr. at gene 5' and 3'	Dnd41	blood
24	chr12:122248400-122249200	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr12:122248400-122249200	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr12:122248400-122249200	Transcr. at gene 5' and 3'	Brain Germinal Matrix	brain
27	chr12:122248400-122249200	Genic enhancers	Fetal Intestine Small	intestine
28	chr12:122248400-122249200	Genic enhancers	Placenta	Placenta
29	chr12:122248400-122249200	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
30	chr12:122248400-122249200	Genic enhancers	HMEC	breast
31	chr12:122248400-122249200	Genic enhancers	NH-A	brain
32	chr12:122248400-122249400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr12:122248400-122249400	Genic enhancers	Primary B cells from cord blood	blood
34	chr12:122248400-122249400	Genic enhancers	Primary B cells from peripheral blood	blood
35	chr12:122248400-122249400	Genic enhancers	Adipose Nuclei	Adipose
36	chr12:122248400-122249400	Genic enhancers	Brain Cingulate Gyrus	brain
37	chr12:122248400-122249400	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
38	chr12:122248600-122249200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
39	chr12:122248600-122249200	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
40	chr12:122248600-122249200	Genic enhancers	Brain Inferior Temporal Lobe	brain
41	chr12:122248600-122249200	Genic enhancers	Fetal Intestine Large	intestine
42	chr12:122248600-122249200	Transcr. at gene 5' and 3'	Hela-S3	cervix
43	chr12:122248600-122249400	Transcr. at gene 5' and 3'	Primary T helper cells fromperipheralblood	blood
44	chr12:122248600-122249400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr12:122248600-122249400	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr12:122248600-122249400	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
47	chr12:122248600-122249400	Genic enhancers	HUVEC	blood vessel
48	chr12:122248600-122249600	Genic enhancers	Lung	lung
49	chr12:122248600-122249600	Genic enhancers	Sigmoid Colon	Sigmoid Colon
50	chr12:122248600-122249600	Transcr. at gene 5' and 3'	K562	blood

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