Variant report

Variant	rs4657476
Chromosome Location	chr1:165732661-165732662
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:165702257..165704580-chr1:165731133..165732717,2	K562	blood:
2	chr1:165731771..165733525-chr1:165736901..165738837,2	K562	blood:
3	chr1:165730777..165733334-chr1:165795438..165798730,3	K562	blood:
4	chr1:165727367..165730301-chr1:165730558..165733503,2	MCF-7	breast:
5	chr1:165730442..165735280-chr1:165736024..165740207,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143179	Chromatin interaction
ENSG00000143183	Chromatin interaction
ENSG00000224358	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10800135	1.00[JPT][hapmap]
rs10800153	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800154	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10800155	1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10918274	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12133745	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12403369	1.00[JPT][hapmap]
rs12691499	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12691500	0.86[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];0.89[YRI][hapmap]
rs2790049	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2790052	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2790053	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[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[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28504591	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4233408	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4537525	1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4603103	0.81[AFR][1000 genomes];0.94[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];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657471	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4657472	0.83[ASN][1000 genomes]
rs4657474	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4657475	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657477	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426936	0.80[AMR][1000 genomes]
rs6660601	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6662839	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668108	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668885	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6696454	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71628393	0.83[ASN][1000 genomes]
rs7518099	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7524755	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7528177	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7555523	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]

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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4657476	NDUFS2	cis	cerebellum	SCAN
rs4657476	MAEL	cis	cerebellum	SCAN
rs4657476	ADCY10	cis	parietal	SCAN
rs4657476	ARHGAP30	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165687600-165737600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:165694600-165736800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr1:165711200-165736200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:165712200-165737000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:165712600-165737000	Weak transcription	Colonic Mucosa	Colon
6	chr1:165713400-165733600	Weak transcription	NHEK	skin
7	chr1:165713600-165737000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:165720800-165733400	Weak transcription	A549	lung
9	chr1:165721800-165732800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr1:165721800-165732800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:165721800-165734800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:165721800-165734800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr1:165721800-165734800	Weak transcription	Esophagus	oesophagus
14	chr1:165721800-165735200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr1:165721800-165736600	Weak transcription	Stomach Mucosa	stomach
16	chr1:165721800-165737000	Weak transcription	Fetal Brain Male	brain
17	chr1:165721800-165737000	Weak transcription	Fetal Heart	heart
18	chr1:165721800-165737000	Weak transcription	Right Atrium	heart
19	chr1:165721800-165737200	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr1:165721800-165737600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:165722400-165732800	Weak transcription	HepG2	liver
22	chr1:165722400-165735000	Weak transcription	HSMMtube	muscle
23	chr1:165722600-165733400	Weak transcription	Brain Anterior Caudate	brain
24	chr1:165722600-165733600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr1:165722600-165736800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:165722800-165734800	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr1:165723000-165736800	Weak transcription	Spleen	Spleen
28	chr1:165723200-165732800	Weak transcription	Pancreas	Pancrea
29	chr1:165723200-165736800	Weak transcription	Colon Smooth Muscle	Colon
30	chr1:165723400-165734800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:165723600-165732800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr1:165723600-165733600	Weak transcription	Brain Angular Gyrus	brain
33	chr1:165723600-165735600	Weak transcription	Brain Germinal Matrix	brain
34	chr1:165723800-165733400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr1:165723800-165733800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr1:165724000-165733800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr1:165724200-165732800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr1:165724200-165732800	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr1:165724200-165733600	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr1:165724200-165733600	Weak transcription	Brain Hippocampus Middle	brain
41	chr1:165724200-165733600	Weak transcription	HUVEC	blood vessel
42	chr1:165725000-165732800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr1:165725200-165733600	Weak transcription	Small Intestine	intestine
44	chr1:165725800-165734200	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr1:165726400-165736800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr1:165726800-165732800	Strong transcription	Duodenum Mucosa	Duodenum
47	chr1:165726800-165736800	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr1:165726800-165737000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:165727000-165736800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:165727400-165732800	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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