Variant report

Variant	rs1991498
Chromosome Location	chr5:54170032-54170033
allele	G/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	NFIC	chr5:54170024-54170870	ECC-1	luminal epithelium:	n/a	n/a
2	EP300	chr5:54170012-54170769	ECC-1	luminal epithelium:	n/a	n/a
3	FOXM1	chr5:54170005-54170708	ECC-1	luminal epithelium:	n/a	n/a
4	TCF7L2	chr5:54170009-54170825	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
ENSG00000232517	TF binding region
ENSG00000249843	TF binding region

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10044930	0.86[ASN][1000 genomes]
rs1005622	0.87[CEU][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10940430	0.83[AFR][1000 genomes]
rs13161386	0.81[EUR][1000 genomes]
rs13161718	0.81[EUR][1000 genomes]
rs1560167	0.87[CEU][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1965716	0.97[ASN][1000 genomes]
rs1988528	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2017318	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2017540	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2407758	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2897758	0.93[ASN][1000 genomes]
rs3935813	0.81[ASN][1000 genomes]
rs4074332	0.87[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs4315891	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4320216	0.87[CEU][hapmap];0.83[AFR][1000 genomes]
rs4373237	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4407587	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4446420	0.90[ASN][1000 genomes]
rs4865586	0.85[CEU][hapmap];0.93[CHB][hapmap];0.87[JPT][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4865587	0.90[ASN][1000 genomes]
rs4865881	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs4865883	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6860824	0.85[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.95[EUR][1000 genomes]
rs6891667	0.81[ASN][1000 genomes]
rs6893903	0.90[EUR][1000 genomes]
rs734097	0.92[ASN][1000 genomes]
rs7448996	0.81[ASN][1000 genomes]
rs7708368	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7734613	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs976645	0.89[ASN][1000 genomes]
rs981978	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[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	nsv830300	chr5:54056300-54257344	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv3358092	chr5:54077828-54189150	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv598179	chr5:54156269-54192823	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:54163400-54170200	Weak transcription	Fetal Lung	lung
2	chr5:54167200-54170200	Weak transcription	Stomach Mucosa	stomach
3	chr5:54168400-54170400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr5:54168400-54171800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr5:54168600-54175600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr5:54169000-54171000	Enhancers	HUVEC	blood vessel
7	chr5:54169200-54170600	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr5:54169400-54171000	Enhancers	Osteobl	bone
9	chr5:54169400-54171400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr5:54169400-54171800	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr5:54169600-54170200	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr5:54169600-54170200	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr5:54169600-54171000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr5:54169600-54171000	Enhancers	Adipose Nuclei	Adipose
15	chr5:54169600-54171400	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr5:54169600-54171400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr5:54169600-54171400	Enhancers	Hela-S3	cervix
18	chr5:54169800-54170200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
19	chr5:54169800-54170200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr5:54169800-54170800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr5:54169800-54171000	Enhancers	Liver	Liver
22	chr5:54169800-54171200	Weak transcription	Left Ventricle	heart
23	chr5:54170000-54170400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr5:54170000-54171200	Enhancers	Monocytes-CD14+_RO01746	blood
25	chr5:54170000-54171400	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr5:54170000-54171400	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr5:54170000-54171400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr5:54170000-54178800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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