Variant report

Variant	rs59554455
Chromosome Location	chr12:64174273-64174274
allele	A/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	POLR2A	chr12:64173495-64174313	IMR90	lung:	n/a	n/a
2	POLR2A	chr12:64173559-64174392	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr12:64173375-64174391	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr12:64173377-64174513	GM12892	blood:	n/a	n/a
5	SIN3AK20	chr12:64173535-64174401	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr12:64173310-64174373	PFSK-1	brain:	n/a	n/a
7	POLR2A	chr12:64173316-64174306	GM18526	blood:	n/a	n/a
8	ELK1	chr12:64173646-64174435	K562	blood:	n/a	n/a
9	SIN3AK20	chr12:64173756-64174308	H1-hESC	embryonic stem cell:	n/a	n/a
10	MYC	chr12:64173621-64174365	K562	blood:	n/a	chr12:64174158-64174171 chr12:64174158-64174168 chr12:64174160-64174167 chr12:64174162-64174169
11	POLR2A	chr12:64173566-64174538	GM12878	blood:	n/a	n/a
12	CHD2	chr12:64173285-64174347	GM12878	blood:	n/a	chr12:64173564-64173574
13	POLR2A	chr12:64173314-64174377	GM18951	blood:	n/a	n/a
14	MYC	chr12:64174039-64174317	Hela-S3	cervix:	n/a	chr12:64174158-64174171 chr12:64174158-64174168 chr12:64174160-64174167 chr12:64174162-64174169
15	SIN3A	chr12:64173326-64174528	H1-hESC	embryonic stem cell:	n/a	chr12:64173958-64173969 chr12:64173605-64173614
16	RUNX3	chr12:64173534-64174407	GM12878	blood:	n/a	n/a
17	TCF12	chr12:64173426-64174481	ECC-1	luminal epithelium:	n/a	chr12:64173955-64173965
18	SIN3AK20	chr12:64173330-64174526	MCF-7	breast:	n/a	n/a
19	CHD2	chr12:64173411-64174368	Hela-S3	cervix:	n/a	chr12:64173564-64173574
20	GABPA	chr12:64173472-64174422	A549	lung:	n/a	chr12:64173550-64173559
21	POLR2A	chr12:64173151-64174323	U87	brain:	n/a	n/a
22	BHLHE40	chr12:64173351-64174319	K562	blood:	n/a	n/a
23	POLR2A	chr12:64173292-64174332	GM12878	blood:	n/a	n/a
24	RELA	chr12:64173324-64174332	GM15510	blood:	n/a	n/a
25	MAX	chr12:64173140-64174536	A549	lung:	n/a	chr12:64174158-64174171 chr12:64174158-64174168 chr12:64174160-64174167 chr12:64173548-64173558 chr12:64174162-64174169
26	POLR2A	chr12:64173259-64174481	SK-N-MC	brain:	n/a	n/a
27	POLR2A	chr12:64173169-64175918	MCF10A-Er-Src	breast:	n/a	n/a
28	MAX	chr12:64173336-64174377	Hela-S3	cervix:	n/a	chr12:64174158-64174171 chr12:64174158-64174168 chr12:64174160-64174167 chr12:64173548-64173558 chr12:64174162-64174169
29	STAT3	chr12:64174057-64174282	MCF10A-Er-Src	breast:	n/a	n/a
30	NFIC	chr12:64173623-64174406	GM12878	blood:	n/a	n/a
31	MAX	chr12:64173870-64174499	H1-hESC	embryonic stem cell:	n/a	chr12:64174158-64174171 chr12:64174158-64174168 chr12:64174160-64174167 chr12:64174162-64174169
32	ATF3	chr12:64173856-64174492	A549	lung:	n/a	chr12:64174431-64174441
33	MAX	chr12:64173333-64174455	HCT-116	colon:	n/a	chr12:64174158-64174171 chr12:64174158-64174168 chr12:64174160-64174167 chr12:64173548-64173558 chr12:64174162-64174169
34	GABPA	chr12:64173321-64174503	MCF-7	breast:	n/a	chr12:64173550-64173559
35	E2F6	chr12:64173247-64174587	A549	lung:	n/a	chr12:64173550-64173559 chr12:64173554-64173564
36	E2F6	chr12:64173657-64174563	H1-hESC	embryonic stem cell:	n/a	n/a
37	MYC	chr12:64173395-64174378	Hela-S3	cervix:	n/a	chr12:64174158-64174171 chr12:64174158-64174168 chr12:64174160-64174167 chr12:64173548-64173558 chr12:64174162-64174169
38	POLR2A	chr12:64173255-64174304	A549	lung:	n/a	n/a
39	NR2F2	chr12:64173519-64174284	K562	blood:	n/a	n/a
40	POLR2A	chr12:64173311-64174273	K562	blood:	n/a	n/a
41	ZBTB7A	chr12:64173101-64174370	ECC-1	luminal epithelium:	n/a	n/a
42	HA-E2F1	chr12:64173622-64174427	MCF-7	breast:	n/a	n/a
43	STAT3	chr12:64174060-64174391	MCF10A-Er-Src	breast:	n/a	chr12:64174369-64174380
44	POLR2A	chr12:64173304-64174413	K562	blood:	n/a	n/a
45	ELF1	chr12:64173190-64174418	MCF-7	breast:	n/a	n/a
46	POLR2A	chr12:64173348-64174382	H1-hESC	embryonic stem cell:	n/a	n/a
47	BCLAF1	chr12:64173582-64174443	GM12878	blood:	n/a	chr12:64173951-64173964
48	POLR2A	chr12:64173254-64174330	ECC-1	luminal epithelium:	n/a	n/a
49	POLR2A	chr12:64173405-64174348	H1-neurons	neurons:	n/a	n/a
50	POLR2A	chr12:64173574-64174354	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:64172533..64176121-chr12:64194832..64198679,5	K562	blood:
2	chr12:64174103..64174726-chr5:180650314..180651063,2	Hela-S3	cervix:
3	chr12:64172395..64175865-chr12:64176316..64181928,12	K562	blood:
4	chr12:64172631..64179011-chr12:64187703..64190145,6	MCF-7	breast:
5	chr12:64172589..64175160-chr12:64189373..64193026,5	MCF-7	breast:
6	chr12:64173978..64177817-chr12:64182120..64184728,4	K562	blood:
7	chr12:64172802..64174995-chr12:64236940..64239856,2	MCF-7	breast:

Variant related genes	Relation type
TMEM5	TF binding region
ENSG00000249753	Chromatin interaction
ENSG00000146063	Chromatin interaction
ENSG00000196935	Chromatin interaction
ENSG00000118600	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11175161	0.93[EUR][1000 genomes]
rs11175166	0.93[EUR][1000 genomes]
rs12582841	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2336002	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4762998	0.87[EUR][1000 genomes]
rs4762999	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4763000	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58158451	0.93[EUR][1000 genomes]
rs60631306	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61440913	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73311798	0.93[EUR][1000 genomes]
rs870799	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs931911	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046836	chr12:63392391-64377169	Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	esv2759905	chr12:63901801-64252172	Bivalent Enhancer Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	esv2758312	chr12:63910416-64252172	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv899171	chr12:63916682-64202233	Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv430514	chr12:63939733-64183598	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv2751110	chr12:63939733-64274680	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv832441	chr12:64063776-64252172	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	esv3449572	chr12:64174108-64174892	Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
9	esv3523514	chr12:64174149-64174848	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
10	esv3523515	chr12:64174149-64174848	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
11	esv3488086	chr12:64174181-64174924	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
12	esv3488097	chr12:64174181-64174924	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:64172800-64174400	Active TSS	Primary T helper naive cells from peripheral blood	blood
2	chr12:64172800-64174400	Active TSS	Skeletal Muscle Female	skeletal muscle
3	chr12:64172800-64174600	Active TSS	Brain Anterior Caudate	brain
4	chr12:64172800-64175200	Active TSS	K562	blood
5	chr12:64173000-64174400	Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr12:64173000-64174400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr12:64173000-64174400	Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr12:64173000-64174400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr12:64173000-64174400	Active TSS	Brain Cingulate Gyrus	brain
10	chr12:64173000-64174400	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr12:64173000-64174600	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr12:64173000-64174600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr12:64173000-64174600	Active TSS	Brain Angular Gyrus	brain
14	chr12:64173000-64174600	Active TSS	Stomach Smooth Muscle	stomach
15	chr12:64173000-64174800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:64173000-64174800	Active TSS	Duodenum Smooth Muscle	Duodenum
17	chr12:64173000-64174800	Active TSS	GM12878-XiMat	blood
18	chr12:64173000-64174800	Active TSS	NHDF-Ad	bronchial
19	chr12:64173000-64175000	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr12:64173000-64175000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr12:64173000-64175000	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr12:64173000-64175000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr12:64173200-64174400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr12:64173200-64174400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr12:64173200-64174400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr12:64173200-64174400	Active TSS	H9 Cell Line	embryonic stem cell
27	chr12:64173200-64174400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr12:64173200-64174400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr12:64173200-64174400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
30	chr12:64173200-64174400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr12:64173200-64174400	Active TSS	Cortex derived primary cultured neurospheres	brain
32	chr12:64173200-64174400	Active TSS	Colon Smooth Muscle	Colon
33	chr12:64173200-64174400	Active TSS	Esophagus	oesophagus
34	chr12:64173200-64174400	Active TSS	Gastric	stomach
35	chr12:64173200-64174400	Active TSS	Left Ventricle	heart
36	chr12:64173200-64174400	Active TSS	Lung	lung
37	chr12:64173200-64174400	Active TSS	Placenta Amnion	Placenta Amnion
38	chr12:64173200-64174400	Active TSS	Small Intestine	intestine
39	chr12:64173200-64174600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr12:64173200-64174600	Active TSS	H1 Cell Line	embryonic stem cell
41	chr12:64173200-64174600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr12:64173200-64174600	Active TSS	Aorta	Aorta
43	chr12:64173200-64174600	Active TSS	Brain Substantia Nigra	brain
44	chr12:64173200-64174600	Active TSS	Colonic Mucosa	Colon
45	chr12:64173200-64174600	Active TSS	Fetal Brain Male	brain
46	chr12:64173200-64174600	Active TSS	Fetal Brain Female	brain
47	chr12:64173200-64174600	Active TSS	Fetal Intestine Large	intestine
48	chr12:64173200-64174600	Active TSS	Fetal Muscle Trunk	muscle
49	chr12:64173200-64174600	Active TSS	Fetal Muscle Leg	muscle
50	chr12:64173200-64174600	Active TSS	Psoas Muscle	Psoas

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