Variant report

Variant	rs12123827
Chromosome Location	chr1:180213860-180213861
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	ESR1	chr1:180213765-180214295	ECC-1	luminal epithelium:	n/a	n/a
2	ESR1	chr1:180213796-180214328	ECC-1	luminal epithelium:	n/a	n/a
3	ZNF263	chr1:180213723-180214507	HEK293-T-REx	kidney:	n/a	chr1:180214270-180214291 chr1:180214281-180214290
4	CTBP2	chr1:180213745-180214464	H1-hESC	embryonic stem cell:	n/a	n/a
5	ESR1	chr1:180213776-180214291	ECC-1	luminal epithelium:	n/a	n/a
6	ESR1	chr1:180213710-180214369	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:180199784..180201302-chr1:180212906..180214774,2	MCF-7	breast:
2	chr1:180198334..180202186-chr1:180213057..180215883,3	K562	blood:
3	chr1:180198334..180201328-chr1:180213324..180215883,2	K562	blood:
4	chr1:180213073..180215826-chr1:180222774..180224846,2	K562	blood:

Variant related genes	Relation type
LHX4	TF binding region
ENSG00000121454	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11583176	0.80[ASN][1000 genomes]
rs11584346	0.82[ASN][1000 genomes]
rs12121448	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12122922	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124504	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124616	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12134787	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12135275	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12135955	0.92[ASN][1000 genomes]
rs12406995	0.99[ASN][1000 genomes]
rs12409555	0.99[ASN][1000 genomes]
rs12752192	0.82[ASN][1000 genomes]
rs28432298	0.99[ASN][1000 genomes]
rs28457118	0.93[ASN][1000 genomes]
rs357075	0.99[ASN][1000 genomes]
rs357076	0.99[ASN][1000 genomes]
rs357078	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3842831	0.86[ASN][1000 genomes]
rs3856050	0.85[ASN][1000 genomes]
rs3911333	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3911334	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3911335	0.92[ASN][1000 genomes]
rs3911336	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652487	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4652488	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4652489	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4652490	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652491	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56028446	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57664116	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59949838	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60046979	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61080341	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61809112	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61809130	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61809133	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61809134	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425616	0.81[ASN][1000 genomes]
rs6673375	0.92[ASN][1000 genomes]
rs7541555	0.99[ASN][1000 genomes]
rs7541647	0.99[ASN][1000 genomes]
rs7551929	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1003739	chr1:180027760-180483292	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv535217	chr1:180027760-180483292	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv1012558	chr1:180027960-180217613	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers 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
5	nsv535218	chr1:180027960-180217613	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv497930	chr1:180031321-180220723	Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv533073	chr1:180031328-180217612	Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer 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
8	nsv916937	chr1:180031328-180220685	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS 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
9	nsv1007590	chr1:180121480-180236452	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
10	nsv999104	chr1:180121480-180242659	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
11	nsv1002133	chr1:180127036-180230081	Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
12	nsv999182	chr1:180127616-180236452	Genic enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
13	nsv1005512	chr1:180127616-180242659	Weak transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
14	nsv832004	chr1:180128502-180335540	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
15	nsv1012145	chr1:180132688-180236452	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
16	nsv466239	chr1:180145978-180268476	Bivalent Enhancer ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
17	nsv548345	chr1:180145978-180268476	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
18	nsv1005073	chr1:180152550-180250783	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
19	nsv535219	chr1:180152550-180250783	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
20	nsv1001477	chr1:180172903-180298287	Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
21	nsv535220	chr1:180172903-180298287	Bivalent Enhancer ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
22	nsv498075	chr1:180179441-180278544	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
23	nsv872575	chr1:180186713-180238243	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180208200-180214000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:180209000-180214800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:180210600-180214200	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr1:180211200-180214400	Enhancers	HUES48 Cell Line	embryonic stem cell
5	chr1:180211600-180214000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:180211800-180216400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:180212000-180214000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:180212600-180216200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr1:180213000-180214000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr1:180213000-180214000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr1:180213000-180215800	Weak transcription	A549	lung
12	chr1:180213200-180214000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr1:180213600-180214200	Enhancers	Rectal Mucosa Donor 29	rectum
14	chr1:180213600-180225800	Weak transcription	Right Atrium	heart
15	chr1:180213800-180214000	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:180213800-180214000	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
17	chr1:180213800-180214000	Bivalent Enhancer	HepG2	liver
18	chr1:180213800-180214200	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr1:180213800-180214400	Enhancers	Duodenum Mucosa	Duodenum
20	chr1:180213800-180214600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr1:180213800-180214600	Enhancers	HUES6 Cell Line	embryonic stem cell

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