Variant report

Variant	rs1360554
Chromosome Location	chr1:155473356-155473357
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:155466285..155469139-chr1:155473048..155474657,2	K562	blood:
2	chr1:155472513..155474941-chr1:155483615..155485164,2	MCF-7	breast:
3	chr1:155473340..155475715-chr1:155533931..155535804,2	K562	blood:

Extended variants
information (count: 74 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10752611	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.94[ASN][1000 genomes]
rs10796943	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs10796945	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.92[ASN][1000 genomes]
rs10796946	0.92[ASN][1000 genomes]
rs10796947	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10908463	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs10908465	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.90[ASN][1000 genomes]
rs10908466	0.92[ASN][1000 genomes]
rs10908467	0.92[ASN][1000 genomes]
rs10908469	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10908470	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.93[ASN][1000 genomes]
rs10908471	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10908472	0.93[ASN][1000 genomes]
rs10908479	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs11264359	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs11264361	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs11264363	0.83[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs11264367	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11264369	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs11264371	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11264372	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11264374	0.92[ASN][1000 genomes]
rs11264375	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.90[ASN][1000 genomes]
rs11264380	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.94[ASN][1000 genomes]
rs11264381	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.93[ASN][1000 genomes]
rs11264383	0.94[ASN][1000 genomes]
rs11264386	0.87[ASN][1000 genomes]
rs11264387	1.00[CHB][hapmap];0.86[CHD][hapmap];0.83[JPT][hapmap];0.82[TSI][hapmap];0.81[ASN][1000 genomes]
rs11582072	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12026638	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.90[ASN][1000 genomes]
rs12028416	0.90[ASN][1000 genomes]
rs12030596	0.94[ASN][1000 genomes]
rs12035524	0.91[JPT][hapmap]
rs12037824	0.88[ASN][1000 genomes]
rs12041534	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.90[ASN][1000 genomes]
rs12046473	0.86[ASN][1000 genomes]
rs12047756	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs12067371	0.93[ASN][1000 genomes]
rs12079134	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12131079	0.81[AMR][1000 genomes]
rs12143948	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs12239100	0.92[ASN][1000 genomes]
rs12239114	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs12724079	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]
rs12744132	0.91[JPT][hapmap]
rs12746592	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.94[ASN][1000 genomes]
rs1325908	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1556488	0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap]
rs1886905	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]
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]
rs2666826	0.90[JPT][hapmap]
rs348196	0.91[JPT][hapmap]
rs35615695	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3738590	0.80[CHB][hapmap];0.91[JPT][hapmap]
rs3892792	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs475550	0.91[JPT][hapmap];0.83[MEX][hapmap]
rs5005770	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs6427278	0.80[ASN][1000 genomes]
rs6684889	0.96[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6688636	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6696888	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs678157	0.91[JPT][hapmap]
rs7411786	0.93[ASN][1000 genomes]
rs7556102	0.92[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
3	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
4	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
5	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
6	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
7	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
8	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:12)

SNP	Gene	Cis/trans	Tissue	Source
rs1360554	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs1360554	GBAP1	cis	parietal	SCAN
rs1360554	FDPS	Cis_1M	lymphoblastoid	RTeQTL
rs1360554	YY1AP1	cis	cerebellum	SCAN
rs1360554	GBAP1	cis	Artery Tibial	GTEx
rs1360554	C1orf56	cis	parietal	SCAN
rs1360554	HDGF	cis	parietal	SCAN
rs1360554	THEM5	cis	parietal	SCAN
rs1360554	GBA	cis	Esophagus Mucosa	GTEx
rs1360554	BCAN	cis	cerebellum	SCAN
rs1360554	SPRR4	cis	parietal	SCAN
rs1360554	PRUNE	cis	cerebellum	SCAN

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155450000-155483000	Weak transcription	NHLF	lung
2	chr1:155452000-155488800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:155452200-155475000	Weak transcription	K562	blood
4	chr1:155452200-155477400	Weak transcription	Lung	lung
5	chr1:155452200-155481400	Weak transcription	Thymus	Thymus
6	chr1:155452200-155482400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr1:155452400-155483000	Weak transcription	HSMM	muscle
8	chr1:155452400-155505200	Weak transcription	Placenta	Placenta
9	chr1:155453400-155477200	Weak transcription	Dnd41	blood
10	chr1:155457800-155474800	Weak transcription	Fetal Thymus	thymus
11	chr1:155457800-155482400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:155462800-155497400	Weak transcription	Pancreas	Pancrea
13	chr1:155463000-155489400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:155464800-155488800	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr1:155466600-155500600	Weak transcription	Aorta	Aorta
16	chr1:155468400-155477600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr1:155470000-155473400	Weak transcription	A549	lung
18	chr1:155470200-155482000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:155470200-155490800	Weak transcription	NHEK	skin
20	chr1:155470400-155473600	Weak transcription	Stomach Mucosa	stomach
21	chr1:155470400-155477200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:155470400-155478000	Weak transcription	Osteobl	bone
23	chr1:155470400-155481000	Weak transcription	Hela-S3	cervix
24	chr1:155470400-155483000	Weak transcription	NHDF-Ad	bronchial
25	chr1:155470400-155488800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr1:155470400-155489400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:155470400-155492000	Weak transcription	NH-A	brain
28	chr1:155470400-155495000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr1:155470400-155501400	Weak transcription	Fetal Kidney	kidney
30	chr1:155470600-155473400	Weak transcription	Brain Anterior Caudate	brain
31	chr1:155470600-155473400	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr1:155470600-155473600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr1:155470600-155473600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr1:155470600-155473600	Weak transcription	Brain Angular Gyrus	brain
35	chr1:155470600-155473600	Weak transcription	Rectal Smooth Muscle	rectum
36	chr1:155470600-155476200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:155470600-155476200	Weak transcription	Fetal Intestine Small	intestine
38	chr1:155470600-155477400	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr1:155470600-155477400	Weak transcription	Primary hematopoietic stem cells	blood
40	chr1:155470600-155477400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:155470600-155477400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:155470600-155477400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:155470600-155477400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr1:155470600-155477400	Weak transcription	Psoas Muscle	Psoas
45	chr1:155470600-155477600	Weak transcription	Primary T cells from cord blood	blood
46	chr1:155470600-155477600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr1:155470600-155477600	Weak transcription	Right Ventricle	heart
48	chr1:155470600-155477600	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr1:155470600-155477600	Weak transcription	Stomach Smooth Muscle	stomach
50	chr1:155470600-155477800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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