Variant report

Variant	rs61821993
Chromosome Location	chr1:160031540-160031541
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	TEAD4	chr1:160031199-160031553	H1-hESC	embryonic stem cell:	n/a	n/a
2	ZNF143	chr1:160031307-160031750	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr1:160031366-160031565	GM12892	blood:	n/a	chr1:160031460-160031478 chr1:160031463-160031476
4	CTCF	chr1:160031460-160031610	HMEC	breast:	n/a	chr1:160031460-160031478 chr1:160031586-160031607 chr1:160031463-160031476
5	RAD21	chr1:160031344-160031616	H1-hESC	embryonic stem cell:	n/a	chr1:160031464-160031477 chr1:160031461-160031480 chr1:160031466-160031476 chr1:160031585-160031604 chr1:160031466-160031478
6	NR2F2	chr1:160031074-160031728	MCF-7	breast:	n/a	n/a
7	HDAC2	chr1:160031196-160031670	MCF-7	breast:	n/a	n/a
8	CTCF	chr1:160031382-160031546	GM19238	blood:	n/a	chr1:160031460-160031478 chr1:160031463-160031476
9	HDAC2	chr1:160030977-160031694	MCF-7	breast:	n/a	n/a
10	REST	chr1:160031243-160031680	MCF-7	breast:	n/a	chr1:160031350-160031359 chr1:160031495-160031509
11	CTCF	chr1:160031371-160031573	GM12891	blood:	n/a	chr1:160031460-160031478 chr1:160031463-160031476
12	NR2F2	chr1:160031050-160031885	MCF-7	breast:	n/a	n/a
13	CTCF	chr1:160031460-160031610	HEK293	kidney:	n/a	chr1:160031460-160031478 chr1:160031586-160031607 chr1:160031463-160031476
14	CTCF	chr1:160031389-160031551	GM19240	blood:	n/a	chr1:160031460-160031478 chr1:160031463-160031476
15	TCF12	chr1:160030974-160031827	MCF-7	breast:	n/a	n/a
16	CTCF	chr1:160031480-160031630	GM12878	blood:	n/a	chr1:160031586-160031607
17	CTCF	chr1:160031400-160031550	HepG2	liver:	n/a	chr1:160031460-160031478 chr1:160031463-160031476
18	TEAD4	chr1:160031217-160031673	H1-hESC	embryonic stem cell:	n/a	n/a
19	CTCF	chr1:160031391-160031657	MCF-7	breast:	n/a	chr1:160031460-160031478 chr1:160031586-160031607 chr1:160031463-160031476
20	RAD21	chr1:160031303-160031604	H1-hESC	embryonic stem cell:	n/a	chr1:160031464-160031477 chr1:160031461-160031480 chr1:160031466-160031476 chr1:160031585-160031604 chr1:160031466-160031478
21	CTCF	chr1:160031440-160031590	Hela-S3	cervix:	n/a	chr1:160031460-160031478 chr1:160031463-160031476
22	GATA3	chr1:160031117-160031665	MCF-7	breast:	n/a	n/a
23	RAD21	chr1:160031185-160031697	H1-hESC	embryonic stem cell:	n/a	chr1:160031464-160031477 chr1:160031461-160031480 chr1:160031466-160031476 chr1:160031585-160031604 chr1:160031466-160031478
24	SIN3AK20	chr1:160030989-160031743	MCF-7	breast:	n/a	n/a
25	SIN3AK20	chr1:160031066-160031552	MCF-7	breast:	n/a	n/a
26	CTCF	chr1:160031343-160031622	H1-hESC	embryonic stem cell:	n/a	chr1:160031460-160031478 chr1:160031586-160031607 chr1:160031463-160031476
27	RAD21	chr1:160031349-160031611	HepG2	liver:	n/a	chr1:160031464-160031477 chr1:160031461-160031480 chr1:160031466-160031476 chr1:160031585-160031604 chr1:160031466-160031478
28	CTCF	chr1:160031358-160031551	GM19239	blood:	n/a	chr1:160031460-160031478 chr1:160031463-160031476
29	CTCF	chr1:160031384-160031550	MCF-7	breast:	n/a	chr1:160031460-160031478 chr1:160031463-160031476

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:160030967..160031835-chr1:160048113..160049078,4	MCF-7	breast:
2	chr1:160031184..160031924-chr1:160053644..160054461,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225279	TF binding region

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11265317	0.91[EUR][1000 genomes]
rs1131891	0.82[EUR][1000 genomes]
rs1186675	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12402888	0.81[EUR][1000 genomes]
rs12408584	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12727520	0.82[EUR][1000 genomes]
rs41265757	0.82[EUR][1000 genomes]
rs55780668	0.80[EUR][1000 genomes]
rs56211999	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61822013	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61822015	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs970365	0.91[AFR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3327316	chr1:159985477-160151281	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv520189	chr1:160011512-160095625	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv1806746	chr1:160029416-160105927	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases
4	esv1824420	chr1:160029416-160105927	Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv1843994	chr1:160029416-160105927	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv534066	chr1:160029416-160105986	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases
7	esv1794281	chr1:160029416-160111565	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	esv1820784	chr1:160029416-160159395	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
9	nsv534165	chr1:160029416-160187302	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160015000-160032400	Enhancers	Brain Inferior Temporal Lobe	brain
2	chr1:160015400-160031600	Enhancers	Brain Angular Gyrus	brain
3	chr1:160016600-160039800	Weak transcription	Right Atrium	heart
4	chr1:160017000-160031600	Enhancers	Brain Cingulate Gyrus	brain
5	chr1:160019200-160036400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:160026000-160031600	Enhancers	Brain Anterior Caudate	brain
7	chr1:160026000-160031800	Enhancers	Brain Substantia Nigra	brain
8	chr1:160030200-160032800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:160030200-160033000	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr1:160030600-160031600	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr1:160030600-160032800	Enhancers	Fetal Brain Male	brain
12	chr1:160030600-160033200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:160030800-160032600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:160031000-160031600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:160031000-160031800	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr1:160031000-160031800	Enhancers	NHEK	skin
17	chr1:160031000-160032000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:160031000-160032000	Enhancers	HMEC	breast
19	chr1:160031000-160032200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
20	chr1:160031000-160032200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:160031000-160032400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr1:160031000-160032600	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr1:160031000-160032600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:160031000-160033200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
25	chr1:160031000-160033200	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr1:160031000-160033400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:160031000-160037000	Enhancers	HepG2	liver
28	chr1:160031200-160031600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:160031200-160031600	Enhancers	Brain Germinal Matrix	brain
30	chr1:160031200-160031800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr1:160031200-160032000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr1:160031200-160032400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:160031200-160032400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
34	chr1:160031200-160032600	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr1:160031200-160032600	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr1:160031200-160033000	Enhancers	H1 Cell Line	embryonic stem cell
37	chr1:160031200-160033000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:160031200-160033000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr1:160031200-160033000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr1:160031400-160032400	Active TSS	Brain Hippocampus Middle	brain

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