Variant report

Variant	rs2073655
Chromosome Location	chr1:161012590-161012591
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:161012560-161012710	A549	lung:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:160989087..160991942-chr1:161007144..161014242,6	K562	blood:
2	chr1:160989663..160992818-chr1:161011844..161017868,15	MCF-7	breast:
3	chr1:161012196..161017661-chr1:161066183..161070852,8	MCF-7	breast:
4	chr1:161011228..161012764-chr1:161122593..161124625,2	K562	blood:
5	chr1:161012288..161019472-chr1:161047717..161055328,13	MCF-7	breast:
6	chr1:161011663..161014033-chr1:161014079..161015803,2	K562	blood:
7	chr1:161011414..161013032-chr1:161129851..161132212,2	K562	blood:
8	chr1:160988071..160992174-chr1:161007125..161014242,7	K562	blood:
9	chr1:161005808..161012985-chr1:161064732..161070101,9	MCF-7	breast:

No data

Variant related genes	Relation type
TSTD1	TF binding region
USF1	TF binding region
ENSG00000270149	TF binding region
ENSG00000228917	Chromatin interaction
ENSG00000143258	Chromatin interaction
ENSG00000162755	Chromatin interaction
ENSG00000158769	Chromatin interaction
ENSG00000143222	Chromatin interaction
ENSG00000158773	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1044478	0.87[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes]
rs1062826	0.91[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes]
rs1062827	0.91[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.80[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes]
rs11265540	0.81[AMR][1000 genomes]
rs11265542	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11799478	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11799521	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11801591	0.80[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap]
rs11802727	1.00[YRI][hapmap]
rs11807930	0.91[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes]
rs12401336	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12403334	0.88[CHB][hapmap];0.85[CHD][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap]
rs12565932	0.91[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes]
rs1556519	1.00[YRI][hapmap]
rs17384360	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs17388108	0.91[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs1806774	0.83[AMR][1000 genomes]
rs2073656	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2073658	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2243427	0.81[AMR][1000 genomes]
rs2247459	0.91[CEU][hapmap];0.86[CHB][hapmap];0.81[AMR][1000 genomes]
rs2247596	0.91[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap]
rs2247671	0.91[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes]
rs2247790	0.91[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes]
rs2251597	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2251728	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2297219	0.86[AMR][1000 genomes]
rs2297220	0.91[CEU][hapmap];0.93[CHB][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs2297221	0.91[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes]
rs2297222	0.86[CEU][hapmap];0.86[AMR][1000 genomes]
rs2481080	0.91[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.81[AMR][1000 genomes]
rs2481081	0.91[CEU][hapmap];0.88[CHB][hapmap];0.80[JPT][hapmap];0.81[AMR][1000 genomes]
rs2481083	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2481084	0.91[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2481085	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2483145	0.81[AMR][1000 genomes]
rs2774274	0.81[AMR][1000 genomes]
rs2988726	0.81[AMR][1000 genomes]
rs3119321	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3737785	0.87[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes]
rs3737787	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41267947	0.86[AMR][1000 genomes]
rs41267949	0.86[AMR][1000 genomes]
rs41267951	0.86[AMR][1000 genomes]
rs41269993	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4339888	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55728374	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61803664	0.86[AMR][1000 genomes]
rs61803671	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61803672	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72712854	0.83[AMR][1000 genomes]
rs812741	0.81[AMR][1000 genomes]
rs836	0.91[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes]
rs869985	0.91[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv947201	chr1:161006051-161013276	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv3221	chr1:161008175-161052979	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv872492	chr1:161009523-161013152	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2073655	OR10J5	cis	cerebellum	SCAN
rs2073655	PAQR6	cis	cerebellum	SCAN
rs2073655	F11R	Cis_1M	lymphoblastoid	RTeQTL
rs2073655	FCRL1	cis	cerebellum	SCAN
rs2073655	RXFP4	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161007000-161013400	Strong transcription	Cortex derived primary cultured neurospheres	brain
2	chr1:161007400-161013400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr1:161007400-161013400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr1:161007400-161013400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:161007400-161013400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:161007600-161013400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:161008000-161013200	Strong transcription	A549	lung
8	chr1:161008000-161013400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:161008200-161013000	Strong transcription	NHLF	lung
10	chr1:161008800-161012600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr1:161008800-161013000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:161008800-161013400	Strong transcription	Brain Cingulate Gyrus	brain
13	chr1:161008800-161014000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:161009000-161012600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:161009000-161012800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr1:161009000-161012800	Strong transcription	Adipose Nuclei	Adipose
17	chr1:161009000-161013200	Strong transcription	Osteobl	bone
18	chr1:161009000-161013400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr1:161009000-161013400	Strong transcription	Fetal Stomach	stomach
20	chr1:161009000-161014000	Genic enhancers	Primary B cells from peripheral blood	blood
21	chr1:161009200-161012600	Strong transcription	Colon Smooth Muscle	Colon
22	chr1:161009200-161012800	Strong transcription	Aorta	Aorta
23	chr1:161009200-161012800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr1:161009200-161013000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:161009200-161013000	Strong transcription	Brain Substantia Nigra	brain
26	chr1:161009200-161013000	Strong transcription	HSMMtube	muscle
27	chr1:161009200-161013000	Strong transcription	HUVEC	blood vessel
28	chr1:161009200-161013200	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr1:161009200-161013200	Strong transcription	HUES64 Cell Line	embryonic stem cell
30	chr1:161009200-161013200	Strong transcription	Fetal Kidney	kidney
31	chr1:161009200-161013200	Strong transcription	Hela-S3	cervix
32	chr1:161009200-161013200	Strong transcription	HepG2	liver
33	chr1:161009200-161013200	Strong transcription	NH-A	brain
34	chr1:161009200-161013200	Strong transcription	NHDF-Ad	bronchial
35	chr1:161009200-161013200	Strong transcription	NHEK	skin
36	chr1:161009200-161013400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:161009200-161013400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr1:161009200-161013400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr1:161009200-161013400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:161009200-161013400	Strong transcription	Brain Angular Gyrus	brain
41	chr1:161009200-161013400	Strong transcription	Brain Anterior Caudate	brain
42	chr1:161009200-161013400	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr1:161009400-161012800	Strong transcription	Brain Hippocampus Middle	brain
44	chr1:161009400-161012800	Strong transcription	Esophagus	oesophagus
45	chr1:161009400-161012800	Strong transcription	Left Ventricle	heart
46	chr1:161009400-161013000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
47	chr1:161009400-161013000	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr1:161009400-161013000	Strong transcription	Brain Inferior Temporal Lobe	brain
49	chr1:161009400-161013200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr1:161009400-161013200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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