Variant report

Variant	rs7555523
Chromosome Location	chr1:165718979-165718980
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:165717436..165719378-chr1:165795999..165798228,2	K562	blood:

Variant related genes	Relation type
ENSG00000143179	Chromatin interaction
ENSG00000143183	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10800135	1.00[JPT][hapmap]
rs10800153	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800154	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10800155	1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10918274	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12133745	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12403369	1.00[JPT][hapmap]
rs12691499	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12691500	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1547725	0.91[CEU][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs2251768	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2790049	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2790052	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2790053	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814463	0.83[ASN][1000 genomes]
rs2814466	1.00[JPT][hapmap]
rs2814471	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28504591	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4233408	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4537525	1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4603103	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656461	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657471	1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4657472	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4657474	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4657475	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657476	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657477	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426936	0.82[AMR][1000 genomes]
rs6660601	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6662839	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668108	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668885	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6696454	1.00[CEU][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71628393	0.83[ASN][1000 genomes]
rs7518099	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7524755	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7528177	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2756102	chr1:165652342-165877342	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers 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	48 gene(s)	inside rSNPs	diseases
2	nsv1011720	chr1:165669589-165802516	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv518886	chr1:165714187-165741646	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

Variant related diseases (count:2)

Disease	PMID	Source
Intraocular pressure	25173106	GWAS catalog
Intraocular pressure	22570627	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7555523	ARHGAP30	cis	parietal	SCAN
rs7555523	MAEL	cis	cerebellum	SCAN
rs7555523	NDUFS2	cis	cerebellum	SCAN
rs7555523	ADCY10	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165685200-165721600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr1:165687600-165737600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:165694200-165721600	Weak transcription	Aorta	Aorta
4	chr1:165694200-165721600	Weak transcription	Esophagus	oesophagus
5	chr1:165694400-165721600	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr1:165694600-165736800	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr1:165696000-165721600	Weak transcription	Gastric	stomach
8	chr1:165699800-165721600	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr1:165705000-165724800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr1:165707600-165721600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:165708000-165721200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr1:165708200-165721600	Weak transcription	Right Atrium	heart
13	chr1:165708800-165721600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:165709200-165720600	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr1:165710400-165721600	Weak transcription	Stomach Mucosa	stomach
16	chr1:165710400-165727000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:165711200-165721600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr1:165711200-165721600	Weak transcription	Fetal Heart	heart
19	chr1:165711200-165736200	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr1:165711400-165722000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr1:165712000-165719800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:165712000-165721600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:165712000-165721600	Weak transcription	Pancreas	Pancrea
24	chr1:165712000-165721600	Weak transcription	Right Ventricle	heart
25	chr1:165712200-165721600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr1:165712200-165721600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr1:165712200-165721600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr1:165712200-165721600	Weak transcription	Brain Substantia Nigra	brain
29	chr1:165712200-165721600	Weak transcription	Colon Smooth Muscle	Colon
30	chr1:165712200-165721600	Weak transcription	Left Ventricle	heart
31	chr1:165712200-165721600	Weak transcription	Psoas Muscle	Psoas
32	chr1:165712200-165721600	Weak transcription	Spleen	Spleen
33	chr1:165712200-165737000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr1:165712400-165721600	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr1:165712400-165721600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr1:165712400-165721600	Weak transcription	Brain Cingulate Gyrus	brain
37	chr1:165712400-165721600	Weak transcription	Brain Hippocampus Middle	brain
38	chr1:165712400-165721600	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr1:165712400-165722000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr1:165712400-165726800	Weak transcription	Fetal Lung	lung
41	chr1:165712400-165727000	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr1:165712400-165727200	Weak transcription	HMEC	breast
43	chr1:165712600-165720200	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr1:165712600-165721600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr1:165712600-165721600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr1:165712600-165721600	Weak transcription	Fetal Brain Male	brain
47	chr1:165712600-165721600	Weak transcription	Ovary	ovary
48	chr1:165712600-165722000	Weak transcription	Brain Germinal Matrix	brain
49	chr1:165712600-165722600	Weak transcription	HUVEC	blood vessel
50	chr1:165712600-165737000	Weak transcription	Colonic Mucosa	Colon

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