Variant report

Variant	rs539714
Chromosome Location	chr1:85904338-85904339
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HNF4A	chr1:85904117-85904439	HepG2	liver:	n/a	chr1:85904241-85904256
2	HNF4G	chr1:85904036-85904445	HepG2	liver:	n/a	chr1:85904240-85904255
3	HNF4G	chr1:85904037-85904529	HepG2	liver:	n/a	chr1:85904240-85904255
4	MAFK	chr1:85904207-85904459	HepG2	liver:	n/a	n/a
5	MAFF	chr1:85904140-85904455	HepG2	liver:	n/a	n/a
6	HNF4A	chr1:85904085-85904403	HepG2	liver:	n/a	chr1:85904241-85904256
7	CEBPB	chr1:85904162-85904444	HepG2	liver:	n/a	n/a
8	RXRA	chr1:85904057-85904421	HepG2	liver:	n/a	n/a
9	NR2F2	chr1:85904104-85904526	HepG2	liver:	n/a	n/a
10	MAFK	chr1:85904218-85904453	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ENSG00000199459	TF binding region

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1006988	0.88[CEU][hapmap]
rs1006989	0.89[CEU][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs10489510	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10747318	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10782549	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10873701	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10873702	1.00[CEU][hapmap]
rs10873703	0.80[JPT][hapmap]
rs11161611	0.91[YRI][hapmap];0.80[AFR][1000 genomes]
rs1146374	0.91[AFR][1000 genomes]
rs1146378	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs1146383	0.80[CEU][hapmap];0.86[JPT][hapmap]
rs12022248	0.91[ASN][1000 genomes]
rs12029221	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12032315	0.83[ASN][1000 genomes]
rs12033483	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12034249	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12035116	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12038426	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12042780	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12047189	0.90[EUR][1000 genomes]
rs1261681	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1342323	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1357635	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1357636	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1391556	0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1523994	1.00[CEU][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes]
rs1523995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1554597	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs1608537	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17384213	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17388696	0.93[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1965876	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1975755	1.00[CEU][hapmap];0.87[YRI][hapmap]
rs2016104	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2037594	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs2064510	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2124139	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2124140	0.87[ASN][1000 genomes]
rs2177461	1.00[YRI][hapmap]
rs2300633	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2389948	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3851268	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4428939	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4512701	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4631749	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4949889	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4949897	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4949898	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4949899	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs499869	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs506082	0.85[AFR][1000 genomes]
rs561422	0.90[AFR][1000 genomes]
rs600098	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs604974	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs631817	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6420965	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs659070	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6657817	0.80[AFR][1000 genomes]
rs6672870	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6704103	0.91[YRI][hapmap];0.80[AFR][1000 genomes]
rs72722663	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72722671	0.84[ASN][1000 genomes]
rs72722691	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72722692	0.86[AMR][1000 genomes]
rs72724608	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs731194	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7515261	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7539738	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7555670	0.89[CEU][hapmap];0.87[JPT][hapmap];0.88[EUR][1000 genomes]
rs990916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv830470	chr1:85820775-86014080	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85886400-85914200	Weak transcription	HSMMtube	muscle
2	chr1:85892200-85906200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr1:85893800-85906200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr1:85893800-85916800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:85897800-85904800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr1:85899200-85914800	Weak transcription	Esophagus	oesophagus
7	chr1:85901400-85923000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:85902200-85904400	Enhancers	H1 Cell Line	embryonic stem cell
9	chr1:85902400-85905200	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr1:85902400-85905200	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr1:85902400-85905400	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr1:85902400-85906200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:85902600-85912200	Weak transcription	Pancreas	Pancrea
14	chr1:85902800-85904400	Enhancers	H9 Cell Line	embryonic stem cell
15	chr1:85902800-85905400	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr1:85903000-85906000	Weak transcription	Ovary	ovary
17	chr1:85903000-85906800	Weak transcription	Lung	lung
18	chr1:85903400-85907000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:85903600-85904400	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr1:85903600-85904600	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr1:85903600-85904800	Genic enhancers	HSMM	muscle
22	chr1:85903600-85905000	Enhancers	Liver	Liver
23	chr1:85903600-85905200	Enhancers	Fetal Kidney	kidney
24	chr1:85903600-85906600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:85903600-85906800	Enhancers	Adipose Nuclei	Adipose
26	chr1:85903600-85907000	Enhancers	HepG2	liver
27	chr1:85903600-85907200	Enhancers	Muscle Satellite Cultured Cells	--
28	chr1:85903600-85907200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:85903600-85907600	Enhancers	NHDF-Ad	bronchial
30	chr1:85903800-85904400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr1:85903800-85904600	Enhancers	Sigmoid Colon	Sigmoid Colon
32	chr1:85903800-85904600	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr1:85903800-85906800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr1:85903800-85906800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr1:85903800-85907200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr1:85903800-85907400	Enhancers	HUVEC	blood vessel
37	chr1:85903800-85907400	Enhancers	NHLF	lung
38	chr1:85903800-85907400	Enhancers	Osteobl	bone
39	chr1:85904000-85904400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr1:85904200-85904400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:85904200-85904400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr1:85904200-85904400	Enhancers	Duodenum Mucosa	Duodenum
43	chr1:85904200-85904400	Enhancers	Fetal Intestine Small	intestine
44	chr1:85904200-85904400	Enhancers	Left Ventricle	heart
45	chr1:85904200-85904400	Enhancers	Psoas Muscle	Psoas
46	chr1:85904200-85904600	Enhancers	Fetal Intestine Large	intestine
47	chr1:85904200-85904600	Enhancers	Fetal Muscle Leg	muscle
48	chr1:85904200-85904600	Enhancers	Fetal Stomach	stomach
49	chr1:85904200-85905000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
50	chr1:85904200-85905000	Enhancers	HUES48 Cell Line	embryonic stem cell

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