Variant report

Variant	rs11264375
Chromosome Location	chr1:155424065-155424066
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10752611	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10796943	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10796944	0.84[AMR][1000 genomes]
rs10796945	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10796946	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10796947	0.91[ASN][1000 genomes]
rs10908463	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap]
rs10908465	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10908466	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10908467	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10908469	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10908470	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10908471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10908472	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11264359	0.84[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap]
rs11264361	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap]
rs11264363	0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs11264366	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11264367	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs11264369	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs11264370	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11264371	0.93[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11264372	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11264374	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11264380	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11264381	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11264383	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11264386	0.81[ASN][1000 genomes]
rs11264387	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.94[GIH][hapmap];0.83[JPT][hapmap];1.00[TSI][hapmap]
rs11582072	0.91[ASN][1000 genomes]
rs12025532	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12026638	0.92[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12028416	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12030596	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12037824	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12041534	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12046473	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12067371	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12079134	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12081067	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12143948	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs12239100	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12239114	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.80[EUR][1000 genomes]
rs12724079	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12746592	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1325908	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1360554	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.90[ASN][1000 genomes]
rs1556488	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1886905	0.96[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap]
rs2025669	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2048431	0.96[CEU][hapmap];0.81[CHB][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap]
rs2297480	0.88[CEU][hapmap];0.89[CHB][hapmap];0.82[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap]
rs35615695	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.85[ASN][1000 genomes]
rs3892792	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs5005770	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56675301	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6670014	0.84[AMR][1000 genomes]
rs6677385	0.83[AFR][1000 genomes]
rs6684889	0.89[CHB][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs6688636	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.91[ASN][1000 genomes]
rs6692183	0.83[AFR][1000 genomes]
rs66923802	0.86[EUR][1000 genomes]
rs6696888	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.87[ASN][1000 genomes]
rs71517782	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7411786	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7416976	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7556102	0.84[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529709	chr1:155154933-155757219	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	450 gene(s)	inside rSNPs	diseases
2	nsv831636	chr1:155219223-155444864	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
4	esv1799856	chr1:155305059-155534616	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	esv1795662	chr1:155305059-155540660	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	esv1795478	chr1:155334933-155510824	Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv1803551	chr1:155334933-155522572	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	esv1800974	chr1:155367680-155510824	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv872468	chr1:155413304-155549562	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11264375	GBAP1	cis	Artery Tibial	GTEx
rs11264375	SPRR2A	cis	cerebellum	SCAN
rs11264375	GBA	cis	Esophagus Mucosa	GTEx
rs11264375	YY1AP1	cis	parietal	SCAN
rs11264375	YY1AP1	cis	cerebellum	SCAN
rs11264375	ADAM15	cis	multi-tissue	Pritchard
rs11264375	SPRR2D	cis	parietal	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155362200-155433400	Weak transcription	Psoas Muscle	Psoas
2	chr1:155362800-155442400	Weak transcription	Right Ventricle	heart
3	chr1:155364400-155450800	Weak transcription	HUVEC	blood vessel
4	chr1:155367400-155426000	Weak transcription	Stomach Mucosa	stomach
5	chr1:155384800-155425600	Weak transcription	Colon Smooth Muscle	Colon
6	chr1:155402400-155426800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr1:155404600-155441400	Weak transcription	Esophagus	oesophagus
8	chr1:155407600-155425800	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr1:155408400-155428000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:155408600-155444200	Weak transcription	Fetal Brain Male	brain
11	chr1:155408600-155448400	Weak transcription	Fetal Brain Female	brain
12	chr1:155408800-155425000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr1:155408800-155425200	Weak transcription	Brain Hippocampus Middle	brain
14	chr1:155408800-155425200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr1:155408800-155425200	Weak transcription	Brain Substantia Nigra	brain
16	chr1:155408800-155425200	Weak transcription	HSMMtube	muscle
17	chr1:155408800-155425200	Weak transcription	NHDF-Ad	bronchial
18	chr1:155408800-155425400	Weak transcription	Brain Angular Gyrus	brain
19	chr1:155408800-155425400	Weak transcription	Brain Anterior Caudate	brain
20	chr1:155408800-155425400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr1:155408800-155425600	Weak transcription	HepG2	liver
22	chr1:155408800-155425800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr1:155408800-155425800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr1:155408800-155428200	Weak transcription	Gastric	stomach
25	chr1:155408800-155435400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr1:155408800-155437000	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr1:155408800-155441000	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr1:155408800-155441000	Weak transcription	Stomach Smooth Muscle	stomach
29	chr1:155408800-155441200	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr1:155408800-155447600	Weak transcription	Aorta	Aorta
31	chr1:155409000-155425000	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr1:155409000-155427400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr1:155409000-155434200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr1:155409200-155427000	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr1:155409400-155425800	Weak transcription	NHLF	lung
36	chr1:155409400-155426800	Weak transcription	Spleen	Spleen
37	chr1:155409400-155431800	Weak transcription	Fetal Muscle Trunk	muscle
38	chr1:155409600-155426000	Weak transcription	K562	blood
39	chr1:155409600-155426600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr1:155409600-155426800	Weak transcription	Hela-S3	cervix
41	chr1:155412000-155429200	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr1:155412200-155433800	Weak transcription	NHEK	skin
43	chr1:155412200-155436600	Weak transcription	HMEC	breast
44	chr1:155414400-155424600	Strong transcription	Fetal Intestine Small	intestine
45	chr1:155416600-155424400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr1:155416800-155424400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:155416800-155424400	Strong transcription	Liver	Liver
48	chr1:155417200-155424200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr1:155418200-155425200	Weak transcription	HSMM	muscle
50	chr1:155418400-155426200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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