Variant report

Variant	rs397695856
Chromosome Location	chr12:58139254-58139255
allele	-/A
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	chr12:58137594-58141397	MCF10A-Er-Src	breast:	n/a	n/a
2	GABPA	chr12:58138048-58139625	SK-N-SH	brain:	n/a	n/a
3	ATF3	chr12:58138628-58139311	A549	lung:	n/a	chr12:58138719-58138727 chr12:58138708-58138728 chr12:58138717-58138730 chr12:58138716-58138731 chr12:58138718-58138729 chr12:58138718-58138729 chr12:58138717-58138727 chr12:58138716-58138727
4	ZNF384	chr12:58138243-58139573	K562	blood:	n/a	n/a
5	RCOR1	chr12:58137549-58139911	IMR90	lung:	n/a	n/a
6	POLR2A	chr12:58138018-58141554	U87	brain:	n/a	n/a
7	POLR2A	chr12:58138353-58140751	PANC-1	pancreas:	n/a	n/a
8	MAZ	chr12:58137824-58139357	GM12878	blood:	n/a	chr12:58139191-58139201
9	ATF2	chr12:58138004-58139627	H1-hESC	embryonic stem cell:	n/a	chr12:58138716-58138730
10	ELK4	chr12:58138785-58139345	Hela-S3	cervix:	n/a	chr12:58139162-58139171 chr12:58139065-58139073 chr12:58139062-58139073 chr12:58139163-58139171 chr12:58139064-58139073
11	GABPA	chr12:58138266-58139705	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr12:58138231-58140454	HUVEC	blood vessel:	n/a	n/a
13	NFIC	chr12:58138687-58139580	GM12878	blood:	n/a	n/a
14	SIN3AK20	chr12:58138221-58139779	MCF-7	breast:	n/a	n/a
15	RCOR1	chr12:58138146-58139374	Hela-S3	cervix:	n/a	n/a
16	EGR1	chr12:58139077-58139359	K562	blood:	n/a	chr12:58139213-58139227 chr12:58139324-58139337
17	SIN3A	chr12:58138243-58139534	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr12:58137470-58141468	A549	lung:	n/a	n/a
19	USF1	chr12:58138699-58139454	A549	lung:	n/a	n/a
20	RCOR1	chr12:58138222-58139399	GM12878	blood:	n/a	n/a
21	POLR2A	chr12:58138094-58140899	GM12891	blood:	n/a	n/a
22	TAF1	chr12:58138128-58139295	SK-N-SH	brain:	n/a	n/a
23	TBP	chr12:58138268-58139364	H1-hESC	embryonic stem cell:	n/a	n/a
24	FOXM1	chr12:58138035-58139268	GM12878	blood:	n/a	n/a
25	PBX3	chr12:58138117-58139864	SK-N-SH	brain:	n/a	n/a
26	POLR2A	chr12:58138164-58140606	NB4	blood:	n/a	n/a
27	ARID3A	chr12:58138132-58139380	HepG2	liver:	n/a	n/a
28	POLR2A	chr12:58138445-58139808	HepG2	liver:	n/a	n/a
29	POLR2A	chr12:58138172-58140310	Raji	blood:	n/a	n/a
30	GABPA	chr12:58138792-58139386	K562	blood:	n/a	n/a
31	JUN	chr12:58137911-58139853	K562	blood:	n/a	chr12:58138715-58138728 chr12:58138719-58138728
32	POLR2A	chr12:58138326-58141516	HepG2	liver:	n/a	n/a
33	KAP1	chr12:58137675-58139388	U2OS	brain:	n/a	n/a
34	MAZ	chr12:58138225-58139679	Hela-S3	cervix:	n/a	chr12:58139191-58139201
35	POLR2A	chr12:58138078-58140660	HUVEC	blood vessel:	n/a	n/a
36	REST	chr12:58137858-58139630	H1-neurons	neurons:	n/a	n/a
37	RELA	chr12:58138211-58139502	GM15510	blood:	n/a	n/a
38	NFATC1	chr12:58138142-58140471	GM12878	blood:	n/a	n/a
39	CREB1	chr12:58137865-58140264	GM12878	blood:	n/a	chr12:58138717-58138730
40	POLR2A	chr12:58138319-58140617	HUVEC	blood vessel:	n/a	n/a
41	POLR2A	chr12:58138349-58141097	U87	brain:	n/a	n/a
42	MAZ	chr12:58138246-58140431	K562	blood:	n/a	chr12:58139191-58139201
43	EP300	chr12:58138226-58139284	GM12878	blood:	n/a	chr12:58139065-58139072 chr12:58139163-58139170 chr12:58139264-58139278 chr12:58138720-58138728 chr12:58139115-58139122
44	BCL3	chr12:58138251-58139761	GM12878	blood:	n/a	chr12:58139114-58139123 chr12:58139064-58139073
45	POLR2A	chr12:58138116-58141537	PANC-1	pancreas:	n/a	n/a
46	TAF1	chr12:58138119-58139494	ECC-1	luminal epithelium:	n/a	n/a
47	POLR2A	chr12:58137917-58140713	Hela-S3	cervix:	n/a	n/a
48	EGR1	chr12:58139066-58139303	GM12878	blood:	n/a	chr12:58139213-58139227
49	ELK1	chr12:58138517-58139551	GM12878	blood:	n/a	chr12:58139162-58139171 chr12:58139114-58139123 chr12:58139114-58139123 chr12:58139162-58139171 chr12:58139064-58139073 chr12:58139064-58139073
50	JUND	chr12:58138260-58139887	A549	lung:	n/a	chr12:58138719-58138728

No.	Distal block	Cell Line	Cell type
1	chr12:57983992..57986489-chr12:58138776..58141177,2	MCF-7	breast:
2	chr12:57912759..57917021-chr12:58137187..58141030,5	MCF-7	breast:
3	chr12:57929794..57931809-chr12:58137772..58140062,2	MCF-7	breast:
4	chr12:57914556..57917935-chr12:58138142..58139921,3	K562	blood:
5	chr12:57985035..57986943-chr12:58137813..58139906,2	K562	blood:
6	chr12:57984385..57986376-chr12:58138351..58140314,2	K562	blood:
7	chr12:58137583..58140333-chr12:58207188..58209651,2	K562	blood:
8	chr12:57912826..57917389-chr12:58135038..58139778,7	K562	blood:
9	chr12:58138996..58139662-chr6:30293787..30294571,2	HCT-116	colon:
10	chr12:57916512..57918954-chr12:58138893..58140769,2	MCF-7	breast:
11	chr12:57940849..57942387-chr12:58138816..58140678,2	K562	blood:
12	chr12:58086381..58087931-chr12:58138408..58140168,2	K562	blood:
13	chr12:57914544..57916510-chr12:58137621..58139842,2	MCF-7	breast:
14	chr12:58136663..58139289-chr12:58209484..58211140,2	MCF-7	breast:
15	chr12:57480720..57482842-chr12:58137848..58140572,2	MCF-7	breast:
16	chr12:57939918..57942387-chr12:58138816..58141058,2	K562	blood:
17	chr12:57912095..57914310-chr12:58137199..58139977,2	MCF-7	breast:

Variant related genes	Relation type
TSPAN31	TF binding region
AGAP2	TF binding region
ENSG00000175197	Chromatin interaction
ENSG00000175203	Chromatin interaction
ENSG00000166886	Chromatin interaction
ENSG00000231074	Chromatin interaction
ENSG00000135506	Chromatin interaction
ENSG00000204599	Chromatin interaction
ENSG00000135407	Chromatin interaction
ENSG00000166881	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000270604	Chromatin interaction
ENSG00000269903	Chromatin interaction
ENSG00000166908	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
2	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	nsv899121	chr12:58079825-58177292	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv559045	chr12:58112189-58165085	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
5	nsv470296	chr12:58112189-58177292	Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
6	nsv899123	chr12:58118248-58155023	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
7	nsv826384	chr12:58124758-58157850	Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv510601	chr12:58130298-58191925	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
9	nsv470297	chr12:58133256-58202419	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
10	nsv826386	chr12:58135303-58150535	Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Weak transcription	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv973963	chr12:58138245-58145482	Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	22 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	chr12:58137800-58139400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr12:58137800-58139400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
3	chr12:58137800-58139400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr12:58137800-58140000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr12:58138000-58139400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr12:58138000-58139400	Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr12:58138000-58139400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr12:58138000-58139400	Active TSS	Brain Hippocampus Middle	brain
9	chr12:58138000-58139400	Active TSS	Colon Smooth Muscle	Colon
10	chr12:58138000-58139400	Active TSS	Left Ventricle	heart
11	chr12:58138000-58139600	Active TSS	Ovary	ovary
12	chr12:58138000-58139600	Flanking Active TSS	Thymus	Thymus
13	chr12:58138000-58139600	Active TSS	HSMMtube	muscle
14	chr12:58138000-58139600	Active TSS	NHLF	lung
15	chr12:58138000-58139800	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr12:58138000-58139800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr12:58138000-58139800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
18	chr12:58138000-58140000	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr12:58138000-58140000	Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr12:58138000-58140000	Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr12:58138200-58139400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr12:58138200-58139400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr12:58138200-58139400	Active TSS	Cortex derived primary cultured neurospheres	brain
24	chr12:58138200-58139400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr12:58138200-58139400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr12:58138200-58139400	Active TSS	Brain Substantia Nigra	brain
27	chr12:58138200-58139400	Active TSS	Psoas Muscle	Psoas
28	chr12:58138200-58139400	Active TSS	A549	lung
29	chr12:58138200-58139400	Active TSS	HepG2	liver
30	chr12:58138200-58139400	Active TSS	HMEC	breast
31	chr12:58138200-58139400	Active TSS	NH-A	brain
32	chr12:58138200-58139400	Active TSS	NHDF-Ad	bronchial
33	chr12:58138200-58139400	Active TSS	NHEK	skin
34	chr12:58138200-58139600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr12:58138200-58139600	Active TSS	iPS-18 Cell Line	embryonic stem cell
36	chr12:58138200-58139600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr12:58138200-58139600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr12:58138200-58139600	Active TSS	Aorta	Aorta
39	chr12:58138200-58139600	Active TSS	Duodenum Smooth Muscle	Duodenum
40	chr12:58138200-58139600	Active TSS	Small Intestine	intestine
41	chr12:58138200-58139600	Active TSS	HSMM	muscle
42	chr12:58138200-58139800	Active TSS	H9 Cell Line	embryonic stem cell
43	chr12:58138200-58139800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr12:58138200-58139800	Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr12:58138200-58140000	Active TSS	H1 Cell Line	embryonic stem cell
46	chr12:58138200-58140000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr12:58138400-58139400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
48	chr12:58138400-58139400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr12:58138400-58139400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr12:58138400-58139400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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