Variant report

Variant	rs1555833
Chromosome Location	chr1:62732170-62732171
allele	A/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	POLR2A	chr1:62732157-62732277	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr1:62731986-62732250	A549	lung:	n/a	n/a
3	MYC	chr1:62731929-62732257	MCF-7	breast:	n/a	n/a
4	CTCF	chr1:62731963-62732257	GM19239	blood:	n/a	n/a
5	MYC	chr1:62731969-62732279	MCF-7	breast:	n/a	n/a
6	MYC	chr1:62731969-62732262	MCF-7	breast:	n/a	n/a
7	MYC	chr1:62732003-62732172	MCF-7	breast:	n/a	n/a
8	MYC	chr1:62732161-62732198	GM12878	blood:	n/a	n/a
9	POLR2A	chr1:62731875-62732360	MCF-7	breast:	n/a	n/a
10	POLR2A	chr1:62731521-62732409	HepG2	liver:	n/a	n/a
11	CTCF	chr1:62732133-62732177	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr1:62731944-62732319	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
KANK4	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2666503	0.87[ASN][1000 genomes]
rs2666506	0.80[ASN][1000 genomes]
rs2666507	0.80[ASN][1000 genomes]
rs2666508	0.80[ASN][1000 genomes]
rs7516290	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1009398	chr1:62656660-62780644	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1013582	chr1:62723703-62910632	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases
5	esv3408127	chr1:62729964-62734262	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62711600-62737200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:62721000-62739400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr1:62728000-62734800	Weak transcription	Fetal Brain Male	brain
4	chr1:62729000-62737600	Weak transcription	Right Atrium	heart
5	chr1:62729400-62732600	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr1:62729400-62734400	Strong transcription	Placenta Amnion	Placenta Amnion
7	chr1:62729600-62734000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:62729600-62736800	Weak transcription	Fetal Muscle Leg	muscle
9	chr1:62729600-62737400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr1:62729600-62737400	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr1:62729600-62737600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr1:62729600-62737800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr1:62729800-62737400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:62730600-62732400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:62730800-62734000	Strong transcription	Adipose Nuclei	Adipose
16	chr1:62731400-62734600	Strong transcription	Fetal Muscle Trunk	muscle
17	chr1:62731400-62734800	Strong transcription	HepG2	liver
18	chr1:62731600-62732400	Strong transcription	Placenta	Placenta
19	chr1:62731800-62732200	ZNF genes & repeats	Esophagus	oesophagus
20	chr1:62731800-62732400	ZNF genes & repeats	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:62731800-62732400	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr1:62731800-62732400	Strong transcription	Liver	Liver
23	chr1:62731800-62732800	Strong transcription	Fetal Intestine Small	intestine
24	chr1:62731800-62733200	Genic enhancers	Pancreas	Pancrea
25	chr1:62732000-62732200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:62732000-62732200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
27	chr1:62732000-62732200	ZNF genes & repeats	Fetal Lung	lung
28	chr1:62732000-62732200	Genic enhancers	Gastric	stomach
29	chr1:62732000-62732400	Enhancers	H1 Cell Line	embryonic stem cell
30	chr1:62732000-62732400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr1:62732000-62732400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr1:62732000-62732400	ZNF genes & repeats	Fetal Kidney	kidney
33	chr1:62732000-62732400	Enhancers	Lung	lung
34	chr1:62732000-62734000	Genic enhancers	Fetal Stomach	stomach
35	chr1:62732000-62734800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr1:62732000-62734800	Weak transcription	Rectal Smooth Muscle	rectum

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