Variant report

Variant	rs1886905
Chromosome Location	chr1:155372672-155372673
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10752611	0.96[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.89[TSI][hapmap]
rs10796943	0.91[CEU][hapmap];0.82[CHB][hapmap];0.85[TSI][hapmap]
rs10796945	0.88[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.89[TSI][hapmap]
rs10908463	0.87[CEU][hapmap];0.84[CHB][hapmap];0.82[CHD][hapmap];0.82[MEX][hapmap]
rs10908465	0.96[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap]
rs10908469	0.92[CEU][hapmap];0.84[CHB][hapmap];0.91[JPT][hapmap]
rs10908470	0.96[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap]
rs10908471	0.96[CEU][hapmap];0.84[CHB][hapmap];0.91[JPT][hapmap]
rs11264359	0.80[CEU][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap]
rs11264361	0.84[CEU][hapmap];0.84[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap]
rs11264363	0.83[ASW][hapmap];0.81[CEU][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs11264367	0.96[CEU][hapmap];0.84[CHB][hapmap];0.91[JPT][hapmap]
rs11264369	1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes]
rs11264371	0.81[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap]
rs11264372	0.81[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap]
rs11264375	0.96[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap]
rs11264380	0.96[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap]
rs11264381	0.96[CEU][hapmap];0.83[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap]
rs11264387	0.96[CEU][hapmap];0.84[CHB][hapmap];0.89[TSI][hapmap]
rs12026638	0.88[CEU][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.89[TSI][hapmap]
rs12041534	0.96[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap]
rs12079134	0.92[CEU][hapmap];0.84[CHB][hapmap];0.91[JPT][hapmap]
rs12143948	1.00[ASW][hapmap];0.81[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];0.91[MKK][hapmap];0.89[TSI][hapmap];0.84[YRI][hapmap]
rs12239114	0.96[CEU][hapmap];0.84[CHB][hapmap];0.94[CHD][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap]
rs12724079	0.81[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap]
rs12746592	0.96[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap]
rs1325908	1.00[ASW][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.94[LWK][hapmap];0.82[MEX][hapmap];0.88[MKK][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes]
rs1360554	1.00[ASW][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];0.84[YRI][hapmap]
rs1556488	0.96[CEU][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap]
rs2297480	0.84[CEU][hapmap];0.82[MEX][hapmap]
rs35615695	0.81[CEU][hapmap];0.84[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.92[TSI][hapmap]
rs3892792	0.96[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap]
rs5005770	0.96[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap]
rs6684889	0.81[CEU][hapmap]
rs6688636	0.92[ASW][hapmap];0.81[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap]
rs6696888	0.81[CEU][hapmap];0.84[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap]
rs7556102	0.89[CHB][hapmap];0.91[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	nsv872467	chr1:155345641-155377171	Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	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

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs1886905	FDPS	cis	lymphoblastoid	seeQTL
rs1886905	YY1AP1	cis	cerebellum	SCAN
rs1886905	FDPS	Cis_1M	lymphoblastoid	RTeQTL
rs1886905	YY1AP1	cis	parietal	SCAN
rs1886905	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs1886905	GBAP1	cis	Artery Tibial	GTEx
rs1886905	PRUNE	cis	cerebellum	SCAN
rs1886905	LCE1C	cis	parietal	SCAN
rs1886905	GBAP1	cis	parietal	SCAN
rs1886905	SETDB1	cis	parietal	SCAN
rs1886905	GBA	cis	Esophagus Mucosa	GTEx
rs1886905	SPRR2D	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155306200-155375400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:155312400-155407400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:155345600-155403000	Weak transcription	Esophagus	oesophagus
4	chr1:155347400-155407400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:155347600-155376000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:155348200-155373800	Weak transcription	Spleen	Spleen
7	chr1:155348200-155380800	Weak transcription	HMEC	breast
8	chr1:155348200-155386000	Weak transcription	NHEK	skin
9	chr1:155349400-155407600	Weak transcription	Aorta	Aorta
10	chr1:155349800-155390800	Weak transcription	Brain Anterior Caudate	brain
11	chr1:155349800-155403000	Weak transcription	NHLF	lung
12	chr1:155350000-155399200	Weak transcription	Brain Angular Gyrus	brain
13	chr1:155350000-155402400	Weak transcription	Brain Substantia Nigra	brain
14	chr1:155350200-155399200	Weak transcription	NH-A	brain
15	chr1:155357200-155400600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr1:155358200-155398400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr1:155358600-155397000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr1:155359400-155407200	Weak transcription	Pancreas	Pancrea
19	chr1:155359600-155375400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:155361400-155406800	Weak transcription	Fetal Heart	heart
21	chr1:155362200-155384800	Weak transcription	Brain Germinal Matrix	brain
22	chr1:155362200-155433400	Weak transcription	Psoas Muscle	Psoas
23	chr1:155362800-155442400	Weak transcription	Right Ventricle	heart
24	chr1:155363000-155373800	Weak transcription	Left Ventricle	heart
25	chr1:155363000-155375200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:155363000-155407400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:155363200-155373600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr1:155363600-155373200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:155364400-155380200	Weak transcription	HSMM	muscle
30	chr1:155364400-155380400	Weak transcription	HSMMtube	muscle
31	chr1:155364400-155389000	Weak transcription	K562	blood
32	chr1:155364400-155450800	Weak transcription	HUVEC	blood vessel
33	chr1:155364600-155374000	Weak transcription	Osteobl	bone
34	chr1:155364800-155384400	Weak transcription	Colon Smooth Muscle	Colon
35	chr1:155365000-155373800	Weak transcription	Lung	lung
36	chr1:155365000-155389600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr1:155365000-155399000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:155365000-155407800	Weak transcription	Fetal Kidney	kidney
39	chr1:155365200-155373000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr1:155365200-155373000	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr1:155365200-155373600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:155365200-155380800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr1:155365200-155385200	Weak transcription	Brain Hippocampus Middle	brain
44	chr1:155365200-155389400	Weak transcription	A549	lung
45	chr1:155365200-155390800	Weak transcription	Brain Cingulate Gyrus	brain
46	chr1:155365200-155403000	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr1:155365200-155406800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr1:155365200-155407000	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr1:155365400-155373400	Weak transcription	Duodenum Mucosa	Duodenum
50	chr1:155365400-155373800	Weak transcription	Adipose Nuclei	Adipose

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