Variant report

Variant	rs12724079
Chromosome Location	chr1:155433942-155433943
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	chr1:155431476..155435286-chr1:155435557..155439516,4	K562	blood:
2	chr1:155433361..155435191-chr1:155460073..155462340,2	K562	blood:

Extended variants
information (count: 70 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10752611	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10796943	1.00[CHB][hapmap];0.97[ASN][1000 genomes]
rs10796945	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10796946	0.99[ASN][1000 genomes]
rs10796947	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10908463	1.00[CHB][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap]
rs10908465	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10908466	0.99[ASN][1000 genomes]
rs10908467	0.97[ASN][1000 genomes]
rs10908469	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10908470	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10908471	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10908472	0.88[ASN][1000 genomes]
rs11264359	0.95[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap]
rs11264361	1.00[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap]
rs11264362	0.82[AMR][1000 genomes]
rs11264363	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11264367	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11264369	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11264370	0.82[ASN][1000 genomes]
rs11264371	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11264372	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11264374	0.99[ASN][1000 genomes]
rs11264375	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11264380	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[ASN][1000 genomes]
rs11264381	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11264383	0.89[ASN][1000 genomes]
rs11264386	0.82[ASN][1000 genomes]
rs11264387	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs11582072	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12025532	0.84[ASN][1000 genomes]
rs12026638	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12028416	0.97[ASN][1000 genomes]
rs12030596	0.89[ASN][1000 genomes]
rs12037824	0.95[ASN][1000 genomes]
rs12041534	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12046473	0.92[ASN][1000 genomes]
rs12047756	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs12067371	0.98[ASN][1000 genomes]
rs12079134	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12131079	0.83[AMR][1000 genomes]
rs12143948	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap]
rs12239100	0.99[ASN][1000 genomes]
rs12239114	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs12746592	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1325908	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1360554	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1556488	0.95[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap]
rs1886905	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]
rs2048431	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs2175391	0.81[CHB][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap]
rs2297480	0.89[CHB][hapmap]
rs35615695	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3738590	0.80[CHB][hapmap];0.91[JPT][hapmap]
rs3892792	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs5005770	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs6684889	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.81[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6688636	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6696888	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7411786	0.88[ASN][1000 genomes]
rs7556102	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]

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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs12724079	C1orf56	cis	parietal	SCAN
rs12724079	YY1AP1	cis	cerebellum	SCAN
rs12724079	THEM5	cis	parietal	SCAN
rs12724079	HDGF	cis	parietal	SCAN
rs12724079	PRUNE	cis	cerebellum	SCAN
rs12724079	GBAP1	cis	parietal	SCAN
rs12724079	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs12724079	GBA	cis	Esophagus Mucosa	GTEx
rs12724079	FDPS	Cis_1M	lymphoblastoid	RTeQTL
rs12724079	BCAN	cis	cerebellum	SCAN
rs12724079	GBAP1	cis	Artery Tibial	GTEx
rs12724079	YY1AP1	cis	parietal	SCAN
rs12724079	S100A8	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155362800-155442400	Weak transcription	Right Ventricle	heart
2	chr1:155364400-155450800	Weak transcription	HUVEC	blood vessel
3	chr1:155404600-155441400	Weak transcription	Esophagus	oesophagus
4	chr1:155408600-155444200	Weak transcription	Fetal Brain Male	brain
5	chr1:155408600-155448400	Weak transcription	Fetal Brain Female	brain
6	chr1:155408800-155435400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr1:155408800-155437000	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr1:155408800-155441000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr1:155408800-155441000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr1:155408800-155441200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr1:155408800-155447600	Weak transcription	Aorta	Aorta
12	chr1:155409000-155434200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr1:155412200-155436600	Weak transcription	HMEC	breast
14	chr1:155418600-155435400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr1:155419200-155434400	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr1:155420600-155441000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr1:155420800-155439400	Weak transcription	Fetal Kidney	kidney
18	chr1:155421000-155436600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr1:155421600-155435600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr1:155421600-155441000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:155421600-155441600	Weak transcription	Brain Germinal Matrix	brain
22	chr1:155421800-155441200	Weak transcription	Ovary	ovary
23	chr1:155421800-155447800	Weak transcription	Lung	lung
24	chr1:155422800-155436400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr1:155423000-155441200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:155423400-155441200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:155423800-155436400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:155424400-155441000	Weak transcription	Fetal Muscle Leg	muscle
29	chr1:155424600-155462600	Weak transcription	Pancreas	Pancrea
30	chr1:155426200-155436400	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr1:155426200-155441000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr1:155426400-155448000	Weak transcription	Rectal Smooth Muscle	rectum
33	chr1:155426400-155455800	Weak transcription	Stomach Mucosa	stomach
34	chr1:155426800-155436600	Weak transcription	Fetal Heart	heart
35	chr1:155427000-155435600	Weak transcription	NHLF	lung
36	chr1:155427000-155436600	Weak transcription	Brain Angular Gyrus	brain
37	chr1:155427000-155441000	Weak transcription	Small Intestine	intestine
38	chr1:155427200-155437600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr1:155427400-155440600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr1:155427600-155436400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr1:155427600-155441000	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr1:155428000-155436400	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr1:155428000-155436800	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr1:155428200-155436400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr1:155428200-155436400	Weak transcription	Brain Anterior Caudate	brain
46	chr1:155428200-155436600	Weak transcription	Hela-S3	cervix
47	chr1:155428200-155440600	Weak transcription	Brain Cingulate Gyrus	brain
48	chr1:155428200-155441000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr1:155428600-155441200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr1:155428600-155441200	Weak transcription	HepG2	liver

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