Variant report

Variant	rs12032520
Chromosome Location	chr1:153895953-153895954
allele	C/G
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	JUND	chr1:153895525-153896087	H1-hESC	embryonic stem cell:	n/a	n/a
2	GABPA	chr1:153895533-153896004	A549	lung:	n/a	n/a
3	POLR2A	chr1:153894132-153896457	K562	blood:	n/a	n/a
4	POLR2A	chr1:153894792-153896295	MCF-7	breast:	n/a	n/a
5	POLR2A	chr1:153895601-153896607	GM12878	blood:	n/a	n/a
6	WRNIP1	chr1:153895573-153896323	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:153895088-153896391	U87	brain:	n/a	n/a
8	MTA3	chr1:153895442-153896866	GM12878	blood:	n/a	n/a
9	REST	chr1:153895509-153896167	HepG2	liver:	n/a	n/a
10	ATF2	chr1:153895496-153896129	H1-hESC	embryonic stem cell:	n/a	n/a
11	TAF1	chr1:153895759-153896086	GM12891	blood:	n/a	n/a
12	REST	chr1:153895562-153896077	SK-N-SH	brain:	n/a	n/a
13	SMC3	chr1:153895033-153895971	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr1:153895620-153896067	SK-N-SH	brain:	n/a	n/a
15	YY1	chr1:153895036-153896341	HepG2	liver:	n/a	chr1:153895250-153895259 chr1:153895250-153895264 chr1:153895256-153895265 chr1:153895251-153895262
16	POLR2A	chr1:153895569-153896427	HepG2	liver:	n/a	n/a
17	FOSL2	chr1:153895492-153896061	A549	lung:	n/a	n/a
18	ELF1	chr1:153895195-153896434	MCF-7	breast:	n/a	chr1:153895256-153895265 chr1:153895250-153895259
19	GTF2F1	chr1:153895505-153896232	H1-hESC	embryonic stem cell:	n/a	n/a
20	POU2F2	chr1:153895784-153895991	GM12878	blood:	n/a	n/a
21	POLR2A	chr1:153895346-153896262	ECC-1	luminal epithelium:	n/a	n/a
22	SMC3	chr1:153895613-153896338	GM12878	blood:	n/a	n/a
23	SIX5	chr1:153895413-153896534	A549	lung:	n/a	n/a
24	MYC	chr1:153895619-153896125	H1-hESC	embryonic stem cell:	n/a	chr1:153895650-153895660
25	CHD2	chr1:153894963-153896212	HepG2	liver:	n/a	chr1:153895015-153895025
26	SP1	chr1:153895365-153896195	H1-hESC	embryonic stem cell:	n/a	chr1:153895528-153895542 chr1:153895527-153895539 chr1:153895527-153895539 chr1:153895529-153895538 chr1:153895528-153895537 chr1:153895528-153895538
27	RELA	chr1:153895541-153896649	GM19193	blood:	n/a	n/a
28	POLR2A	chr1:153894077-153896211	H1-neurons	neurons:	n/a	n/a
29	POLR2A	chr1:153894917-153896471	ProgFib	skin:	n/a	n/a
30	SIN3AK20	chr1:153893963-153896809	MCF-7	breast:	n/a	n/a
31	TBP	chr1:153894515-153896209	K562	blood:	n/a	n/a
32	RELA	chr1:153895472-153896298	GM10847	blood:	n/a	n/a
33	POLR2A	chr1:153894240-153896509	SK-N-MC	brain:	n/a	n/a
34	REST	chr1:153894266-153896514	H1-neurons	neurons:	n/a	n/a
35	TAF1	chr1:153895434-153896391	PFSK-1	brain:	n/a	n/a
36	TAF1	chr1:153895336-153896375	A549	lung:	n/a	n/a
37	MAFK	chr1:153895761-153896184	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr1:153894202-153896303	GM19193	blood:	n/a	n/a
39	POLR2A	chr1:153894511-153896243	NB4	blood:	n/a	n/a
40	FOXM1	chr1:153895439-153896272	GM12878	blood:	n/a	n/a
41	EBF1	chr1:153895329-153895957	GM12878	blood:	n/a	n/a
42	UBTF	chr1:153895110-153896377	K562	blood:	n/a	n/a
43	SP1	chr1:153895334-153896210	H1-hESC	embryonic stem cell:	n/a	chr1:153895528-153895542 chr1:153895527-153895539 chr1:153895527-153895539 chr1:153895529-153895538 chr1:153895528-153895537 chr1:153895528-153895538
44	POLR2A	chr1:153895376-153896697	PANC-1	pancreas:	n/a	n/a
45	YY1	chr1:153894609-153896202	GM12892	blood:	n/a	chr1:153895250-153895259 chr1:153895250-153895264 chr1:153894991-153895000 chr1:153895256-153895265 chr1:153895251-153895262
46	MAX	chr1:153895020-153896265	SK-N-SH	brain:	n/a	chr1:153895650-153895660
47	PML	chr1:153893808-153896909	GM12878	blood:	n/a	n/a
48	MAFK	chr1:153895450-153896034	Hela-S3	cervix:	n/a	n/a
49	NFIC	chr1:153895430-153896145	HepG2	liver:	n/a	chr1:153895453-153895470 chr1:153895454-153895470
50	POLR2A	chr1:153895340-153896330	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:153876373..153878542-chr1:153895885..153898675,2	MCF-7	breast:
2	chr1:153877108..153878682-chr1:153895765..153897266,2	MCF-7	breast:
3	chr1:153754212..153755933-chr1:153895678..153897558,2	MCF-7	breast:
4	chr1:153746879..153748867-chr1:153894033..153896594,2	K562	blood:
5	chr1:153895740..153897837-chr1:153943889..153946468,2	K562	blood:
6	chr1:153537683..153540046-chr1:153895076..153896651,2	K562	blood:
7	chr1:153893510..153896669-chr1:153958441..153960611,3	K562	blood:
8	chr1:153890756..153897034-chr1:153961597..153964863,14	K562	blood:
9	chr1:153892664..153896587-chr1:153948190..153951187,6	K562	blood:
10	chr1:153747665..153750002-chr1:153895693..153897209,2	MCF-7	breast:
11	chr1:153895897..153896422-chr11:48153597..48154395,2	Hela-S3	cervix:
12	chr1:153895633..153896175-chr1:153949945..153950661,2	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CREB3L4-1	chr1:153895762-153896438	NONHSAT006552

Variant related genes	Relation type
GATAD2B	TF binding region
ENSG00000143545	Chromatin interaction
ENSG00000196754	Chromatin interaction
ENSG00000272654	Chromatin interaction
ENSG00000143543	Chromatin interaction
ENSG00000177954	Chromatin interaction
ENSG00000143554	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11264522	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12023578	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12033532	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12039936	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12043354	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12044455	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12045838	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12726350	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2072704	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2297895	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33998934	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34579266	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34665499	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35170146	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4309017	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4323749	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61804837	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61804838	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61804839	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61805526	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6427334	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7527406	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9427246	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv531892	chr1:153671910-153954090	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
4	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
5	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
6	nsv872450	chr1:153889042-153937513	Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
7	esv3441037	chr1:153893853-153896701	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	esv3384628	chr1:153893928-153896576	Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	esv3436408	chr1:153894528-153895976	Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153893200-153896200	Active TSS	NHDF-Ad	bronchial
2	chr1:153893600-153896400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:153893600-153897000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr1:153893800-153896000	Active TSS	NHLF	lung
5	chr1:153893800-153896200	Active TSS	HSMMtube	muscle
6	chr1:153893800-153896200	Active TSS	K562	blood
7	chr1:153893800-153896400	Active TSS	H1 Cell Line	embryonic stem cell
8	chr1:153893800-153896400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:153893800-153896400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:153893800-153896600	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr1:153893800-153896800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:153893800-153896800	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr1:153893800-153896800	Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr1:153893800-153896800	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr1:153893800-153897000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:153893800-153897400	Active TSS	H9 Cell Line	embryonic stem cell
17	chr1:153894000-153896000	Active TSS	Fetal Muscle Trunk	muscle
18	chr1:153894000-153896000	Active TSS	HSMM	muscle
19	chr1:153894000-153896000	Active TSS	NHEK	skin
20	chr1:153894000-153896400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr1:153894000-153896400	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr1:153894000-153896400	Active TSS	Breast Myoepithelial Primary Cells	Breast
23	chr1:153894000-153896400	Active TSS	Fetal Kidney	kidney
24	chr1:153894000-153896400	Active TSS	Ovary	ovary
25	chr1:153894000-153896600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr1:153894000-153896600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:153894000-153896600	Active TSS	Aorta	Aorta
28	chr1:153894000-153896800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:153894000-153896800	Active TSS	iPS-20b Cell Line	embryonic stem cell
30	chr1:153894000-153896800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr1:153894200-153896200	Active TSS	Fetal Stomach	stomach
32	chr1:153894200-153896600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr1:153894200-153896600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr1:153894200-153896600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr1:153894200-153896800	Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr1:153894200-153896800	Active TSS	HUES64 Cell Line	embryonic stem cell
37	chr1:153894200-153896800	Active TSS	A549	lung
38	chr1:153894400-153896000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr1:153894400-153896000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr1:153894400-153896000	Active TSS	Primary T helper cells PMA-I stimulated	--
41	chr1:153894400-153896000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr1:153894400-153896000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:153894400-153896000	Active TSS	Duodenum Smooth Muscle	Duodenum
44	chr1:153894400-153896000	Active TSS	Fetal Brain Female	brain
45	chr1:153894400-153896000	Active TSS	Rectal Smooth Muscle	rectum
46	chr1:153894400-153896000	Active TSS	Hela-S3	cervix
47	chr1:153894400-153896200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
48	chr1:153894400-153896200	Active TSS	Primary T killer memory cells from peripheral blood	blood
49	chr1:153894400-153896200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr1:153894400-153896200	Active TSS	Brain Anterior Caudate	brain

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