Variant report

Variant	rs1277442
Chromosome Location	chr12:118605571-118605572
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1051470	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];0.82[TSI][hapmap];0.86[ASN][1000 genomes]
rs1151900	0.90[MKK][hapmap];0.95[TSI][hapmap]
rs1277441	1.00[CEU][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.98[EUR][1000 genomes]
rs1622210	0.85[EUR][1000 genomes]
rs1699160	0.84[ASW][hapmap];0.91[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];0.89[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap]
rs1726390	0.83[EUR][1000 genomes]
rs1726392	1.00[CEU][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.90[EUR][1000 genomes]
rs1726407	0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs191626	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2454761	0.84[ASN][1000 genomes]
rs2650175	0.81[EUR][1000 genomes]
rs2936839	0.86[ASN][1000 genomes]
rs353888	0.95[CEU][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs353893	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs353894	0.82[EUR][1000 genomes]
rs353897	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]
rs383371	0.95[CEU][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs428073	0.84[ASW][hapmap];0.87[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap]
rs431038	0.91[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap]
rs556081	0.84[ASW][hapmap];0.91[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap]
rs708865	0.81[EUR][1000 genomes]
rs708867	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs708868	0.95[CEU][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs795474	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs795475	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs795476	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs795478	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs795479	0.86[EUR][1000 genomes]
rs795480	0.83[EUR][1000 genomes]
rs795483	1.00[CEU][hapmap];0.88[YRI][hapmap];0.90[EUR][1000 genomes]
rs795484	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs811247	0.95[CEU][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.86[EUR][1000 genomes]
rs904661	0.82[TSI][hapmap]
rs904662	0.92[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.84[MKK][hapmap];0.82[TSI][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv1054703	chr12:118575000-118638613	Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv541611	chr12:118575000-118638613	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	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
5	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1277442	PLA2G1B	cis	cerebellum	SCAN
rs1277442	PEBP1	cis	cerebellum	SCAN
rs1277442	PEBP1	cis	lymphoblastoid	seeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118576000-118619600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
2	chr12:118576000-118624000	Weak transcription	Stomach Mucosa	stomach
3	chr12:118578200-118611600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:118584000-118627600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr12:118585800-118619000	Weak transcription	HepG2	liver
6	chr12:118586200-118619400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr12:118586600-118613600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:118587600-118611200	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr12:118587600-118619200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr12:118587800-118620000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr12:118589600-118619000	Weak transcription	A549	lung
12	chr12:118590400-118617000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr12:118592600-118619400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:118593200-118619200	Strong transcription	Fetal Brain Female	brain
15	chr12:118593200-118619400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr12:118593200-118619600	Strong transcription	Primary T cells fromperipheralblood	blood
17	chr12:118598200-118620000	Weak transcription	Hela-S3	cervix
18	chr12:118599000-118607800	Weak transcription	Fetal Brain Male	brain
19	chr12:118599200-118608000	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr12:118599400-118607200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr12:118599600-118605600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr12:118599800-118607400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr12:118599800-118607600	Weak transcription	Small Intestine	intestine
24	chr12:118599800-118608000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr12:118599800-118608200	Weak transcription	Colonic Mucosa	Colon
26	chr12:118599800-118608200	Weak transcription	HMEC	breast
27	chr12:118599800-118608400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr12:118599800-118608400	Weak transcription	Colon Smooth Muscle	Colon
29	chr12:118599800-118609800	Weak transcription	Psoas Muscle	Psoas
30	chr12:118599800-118609800	Weak transcription	HUVEC	blood vessel
31	chr12:118599800-118613000	Weak transcription	HSMMtube	muscle
32	chr12:118599800-118625600	Weak transcription	Pancreas	Pancrea
33	chr12:118600000-118605800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr12:118600000-118605800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr12:118600000-118607200	Weak transcription	Esophagus	oesophagus
36	chr12:118600000-118607200	Weak transcription	Fetal Intestine Small	intestine
37	chr12:118600000-118607400	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr12:118600000-118607800	Weak transcription	Spleen	Spleen
39	chr12:118600000-118608000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr12:118600000-118608000	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr12:118600000-118608800	Weak transcription	Gastric	stomach
42	chr12:118600000-118609400	Weak transcription	Right Ventricle	heart
43	chr12:118600000-118609600	Weak transcription	Fetal Heart	heart
44	chr12:118600000-118610000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr12:118600200-118605600	Weak transcription	Brain Angular Gyrus	brain
46	chr12:118600200-118605600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr12:118600200-118607200	Weak transcription	Lung	lung
48	chr12:118600200-118608200	Weak transcription	Aorta	Aorta
49	chr12:118600200-118608200	Weak transcription	Rectal Smooth Muscle	rectum
50	chr12:118600200-118613600	Weak transcription	Fetal Kidney	kidney

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