Variant report

Variant	rs353897
Chromosome Location	chr12:118639841-118639842
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:118639707..118640538-chr12:118813621..118814282,4	MCF-7	breast:
2	chr12:118638724..118640594-chr12:118810784..118812979,2	K562	blood:

Variant related genes	Relation type
ENSG00000111707	Chromatin interaction
ENSG00000270482	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1051470	0.85[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap]
rs1151900	0.82[CEU][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.90[EUR][1000 genomes]
rs1277441	0.95[CEU][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.88[YRI][hapmap];0.83[EUR][1000 genomes]
rs1277442	0.92[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1699160	0.92[ASW][hapmap];0.95[CEU][hapmap];0.87[CHB][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1726390	0.96[EUR][1000 genomes]
rs1726392	0.95[CEU][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap]
rs1726407	0.94[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap]
rs191626	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2454757	0.87[AMR][1000 genomes]
rs2650175	0.91[EUR][1000 genomes]
rs353884	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs353888	1.00[CEU][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs353891	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs353893	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs353894	0.96[EUR][1000 genomes]
rs353895	0.91[EUR][1000 genomes]
rs383371	1.00[CEU][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs411828	0.88[EUR][1000 genomes]
rs424034	0.87[EUR][1000 genomes]
rs428073	0.92[ASW][hapmap];0.91[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs431038	0.95[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs459547	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs461801	0.81[EUR][1000 genomes]
rs464227	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs466600	0.84[AMR][1000 genomes]
rs514826	0.83[ASW][hapmap];0.90[JPT][hapmap];0.89[LWK][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.88[YRI][hapmap]
rs521048	0.91[CEU][hapmap];0.88[GIH][hapmap];0.83[TSI][hapmap]
rs556081	0.92[ASW][hapmap];0.95[CEU][hapmap];0.94[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61945179	0.91[EUR][1000 genomes]
rs708865	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs708867	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs708868	1.00[CEU][hapmap];0.95[TSI][hapmap];0.96[EUR][1000 genomes]
rs795474	0.81[ASN][1000 genomes]
rs795475	0.95[CEU][hapmap]
rs795476	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs795478	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs795479	0.82[EUR][1000 genomes]
rs795483	0.95[CEU][hapmap];0.84[YRI][hapmap]
rs795484	0.92[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.81[EUR][1000 genomes]
rs811247	1.00[CEU][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.94[EUR][1000 genomes]
rs904662	0.85[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap]

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	nsv1053785	chr12:118490955-118874194	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1035497	chr12:118599539-118732144	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv541612	chr12:118599539-118732144	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv524938	chr12:118624736-118740675	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs353897	PEBP1	cis	cerebellum	SCAN
rs353897	SDS	cis	cerebellum	SCAN
rs353897	PEBP1	cis	lymphoblastoid	seeQTL

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118620200-118656400	Weak transcription	HepG2	liver
2	chr12:118621000-118682600	Weak transcription	A549	lung
3	chr12:118622400-118643800	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr12:118622400-118643800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr12:118622400-118646400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr12:118622600-118642000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr12:118623600-118642600	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr12:118625600-118641600	Weak transcription	Stomach Mucosa	stomach
9	chr12:118628400-118697200	Weak transcription	Psoas Muscle	Psoas
10	chr12:118628600-118640200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr12:118628800-118640200	Weak transcription	Fetal Brain Male	brain
12	chr12:118628800-118650000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr12:118628800-118672600	Weak transcription	Colon Smooth Muscle	Colon
14	chr12:118628800-118673000	Weak transcription	NH-A	brain
15	chr12:118629800-118652400	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr12:118630800-118650000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr12:118631200-118640400	Strong transcription	Dnd41	blood
18	chr12:118631200-118642800	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr12:118631200-118643800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr12:118631400-118642400	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr12:118631400-118642600	Strong transcription	Primary B cells from peripheral blood	blood
22	chr12:118634800-118642400	Strong transcription	Primary B cells from cord blood	blood
23	chr12:118635400-118641600	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr12:118635800-118640000	Strong transcription	Primary hematopoietic stem cells	blood
25	chr12:118636800-118658600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr12:118636800-118695000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr12:118637000-118640800	Weak transcription	Hela-S3	cervix
28	chr12:118637000-118652200	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr12:118637200-118640800	Weak transcription	Fetal Muscle Trunk	muscle
30	chr12:118637200-118642400	Weak transcription	Right Ventricle	heart
31	chr12:118637200-118647800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr12:118637200-118648000	Weak transcription	Brain Substantia Nigra	brain
33	chr12:118637200-118654400	Weak transcription	Stomach Smooth Muscle	stomach
34	chr12:118637200-118700600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr12:118637200-118700800	Weak transcription	Fetal Muscle Leg	muscle
36	chr12:118637400-118640600	Weak transcription	Fetal Intestine Small	intestine
37	chr12:118637400-118641200	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr12:118637400-118649200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr12:118637400-118653600	Weak transcription	Ovary	ovary
40	chr12:118637400-118658200	Weak transcription	Brain Anterior Caudate	brain
41	chr12:118637400-118671400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr12:118637400-118672400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr12:118637400-118684200	Weak transcription	Pancreas	Pancrea
44	chr12:118637400-118694200	Weak transcription	Brain Angular Gyrus	brain
45	chr12:118637400-118701400	Weak transcription	Spleen	Spleen
46	chr12:118637400-118703800	Weak transcription	Esophagus	oesophagus
47	chr12:118637400-118724000	Weak transcription	Aorta	Aorta
48	chr12:118637600-118647400	Weak transcription	Thymus	Thymus
49	chr12:118637600-118673000	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr12:118637800-118650000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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