Variant report

Variant	rs34102859
Chromosome Location	chr12:56556389-56556390
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:126)
CpG islands
(count:61)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:126 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:56551094-56558885	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr12:56554227-56556989	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:56551096-56559842	GM12878	blood:	n/a	n/a
4	POLR2A	chr12:56551899-56559978	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr12:56556267-56556909	GM19099	blood:	n/a	n/a
6	POLR2A	chr12:56551937-56557019	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr12:56556194-56556502	GM12878	blood:	n/a	n/a
8	POLR2A	chr12:56550969-56558589	GM12892	blood:	n/a	n/a
9	POLR2A	chr12:56551944-56557093	GM12892	blood:	n/a	n/a
10	POLR2A	chr12:56556172-56557097	Hela-S3	cervix:	n/a	n/a
11	JUND	chr12:56555876-56556576	A549	lung:	n/a	n/a
12	POLR2A	chr12:56551250-56558611	U87	brain:	n/a	n/a
13	HEY1	chr12:56556172-56556606	K562	blood:	n/a	n/a
14	HEY1	chr12:56556204-56556668	K562	blood:	n/a	n/a
15	POLR2A	chr12:56551896-56556539	HCT-116	colon:	n/a	n/a
16	POLR2A	chr12:56551408-56556564	K562	blood:	n/a	n/a
17	POLR2A	chr12:56550856-56557007	HepG2	liver:	n/a	n/a
18	PBX3	chr12:56556174-56556656	A549	lung:	n/a	n/a
19	POLR2A	chr12:56556344-56556418	MCF-7	breast:	n/a	n/a
20	TEAD4	chr12:56556160-56556708	K562	blood:	n/a	n/a
21	POLR2A	chr12:56551369-56560498	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr12:56556197-56556520	A549	lung:	n/a	n/a
23	POLR2A	chr12:56551123-56558578	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr12:56551053-56559864	GM12891	blood:	n/a	n/a
25	POLR2A	chr12:56551393-56557009	K562	blood:	n/a	n/a
26	POLR2A	chr12:56550960-56557121	K562	blood:	n/a	n/a
27	POLR2A	chr12:56555723-56556950	HL-60	blood:	n/a	n/a
28	BCL3	chr12:56551157-56556978	A549	lung:	n/a	chr12:56553213-56553222 chr12:56554315-56554324 chr12:56552652-56552661 chr12:56554170-56554179
29	POLR2A	chr12:56551331-56558611	U87	brain:	n/a	n/a
30	POLR2A	chr12:56551292-56558563	HepG2	liver:	n/a	n/a
31	POLR2A	chr12:56551237-56556498	GM12878	blood:	n/a	n/a
32	MAX	chr12:56556191-56556577	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr12:56553459-56557519	K562	blood:	n/a	n/a
34	PML	chr12:56555047-56556964	K562	blood:	n/a	n/a
35	POLR2A	chr12:56556275-56556896	K562	blood:	n/a	n/a
36	POLR2A	chr12:56555404-56558566	HepG2	liver:	n/a	n/a
37	MTA3	chr12:56556346-56556953	GM12878	blood:	n/a	n/a
38	TCF3	chr12:56556295-56556457	GM12878	blood:	n/a	n/a
39	PBX3	chr12:56556185-56557081	SK-N-SH	brain:	n/a	n/a
40	POLR2A	chr12:56551184-56558544	GM12878	blood:	n/a	n/a
41	POLR2A	chr12:56550944-56560010	GM12892	blood:	n/a	n/a
42	POLR2A	chr12:56550950-56560311	U87	brain:	n/a	n/a
43	POLR2A	chr12:56556208-56556546	GM12878	blood:	n/a	n/a
44	POLR2A	chr12:56550946-56559901	GM12892	blood:	n/a	n/a
45	PML	chr12:56556281-56556907	GM12878	blood:	n/a	n/a
46	NFIC	chr12:56556059-56557110	GM12878	blood:	n/a	n/a
47	POLR2A	chr12:56550849-56560509	H1-hESC	embryonic stem cell:	n/a	n/a
48	ATF2	chr12:56556186-56557137	GM12878	blood:	n/a	n/a
49	ELK1	chr12:56556367-56556402	K562	blood:	n/a	n/a
50	POLR2A	chr12:56551127-56558589	GM18505	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:56556339-56556389	AG09309	skin:	n/a
2	chr12:56556339-56556389	HepG2	liver:	n/a
3	chr12:56556339-56556389	A549	lung:	n/a
4	chr12:56556339-56556389	K562	blood:	n/a
5	chr12:56556339-56556389	HCT-116	colon:	n/a
6	chr12:56556339-56556389	LNCaP	prostate:	n/a
7	chr12:56556339-56556389	NHDF-neo	bronchial:	n/a
8	chr12:56556339-56556389	T-47D	breast:	n/a
9	chr12:56556339-56556389	HAEpiC	amniotic membrane:	n/a
10	chr12:56556339-56556389	GM19239	blood:	n/a
11	chr12:56556339-56556389	IMR90	lung:	fetal
12	chr12:56556339-56556389	HCF	heart:	n/a
13	chr12:56556339-56556389	HL-60	blood:	n/a
14	chr12:56556339-56556389	HNPCEpiC	eye:	n/a
15	chr12:56556339-56556389	GM12892	blood:	n/a
16	chr12:56556339-56556389	GM12891	blood:	n/a
17	chr12:56556339-56556389	AG04449	skin:	fetal
18	chr12:56556339-56556389	ProgFib	skin:	n/a
19	chr12:56556339-56556389	NT2-D1	testis:	n/a
20	chr12:56556339-56556389	HUVEC	blood vessel:	n/a
21	chr12:56556339-56556389	MCF10A-Er-Src	breast:	n/a
22	chr12:56556339-56556389	SK-N-MC	brain:	n/a
23	chr12:56556339-56556389	HRE	kidney:	n/a
24	chr12:56556339-56556389	PFSK-1	brain:	n/a
25	chr12:56556339-56556389	ECC-1	luminal epithelium:	n/a
26	chr12:56556339-56556389	HEK293	kidney:	embryo
27	chr12:56556339-56556389	HEEpiC	esophagus:	n/a
28	chr12:56556339-56556389	HMEC	breast:	n/a
29	chr12:56556339-56556389	Hepatocyte	liver:	n/a
30	chr12:56556339-56556389	HCPEpiC	choroid plexus:	n/a
31	chr12:56556339-56556389	HRCEpiC	kidney:	n/a
32	chr12:56556339-56556389	AG09319	gingival:	n/a
33	chr12:56556339-56556389	RPTEC	kidney:	n/a
34	chr12:56556339-56556389	U87	brain:	n/a
35	chr12:56556339-56556389	SK-N-SH	brain:	n/a
36	chr12:56556339-56556389	NB4	blood:	n/a
37	chr12:56556339-56556389	GM12878	blood:	n/a
38	chr12:56556339-56556389	CMK	blood:	n/a
39	chr12:56556339-56556389	Caco-2	colon:	n/a
40	chr12:56556339-56556389	H1-hESC	embryonic stem cell:	embryo
41	chr12:56556339-56556389	HIPEpiC	eye:	n/a
42	chr12:56556339-56556389	AG10803	skin:	n/a
43	chr12:56556339-56556389	BJ	skin:	n/a
44	chr12:56556339-56556389	MCF-7	breast:	n/a
45	chr12:56556339-56556389	HRPEpiC	eye:	n/a
46	chr12:56556339-56556389	SK-N-SH_RA	brain:	n/a
47	chr12:56556339-56556389	PrEC	prostate:	n/a
48	chr12:56556339-56556389	BE2_C	brain:	n/a
49	chr12:56556339-56556389	SAEC	small airway:	n/a
50	chr12:56556339-56556389	NH-A	brain:	n/a

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56519569..56524417-chr12:56555136..56559386,7	MCF-7	breast:
2	chr12:56507747..56515530-chr12:56549896..56559767,36	MCF-7	breast:
3	chr12:56555640..56556592-chr5:77382006..77382689,2	MCF-7	breast:
4	chr12:56550178..56557145-chr12:56575233..56584234,22	MCF-7	breast:
5	chr12:56555575..56559799-chr12:56572215..56575124,4	MCF-7	breast:
6	chr12:56508092..56528020-chr12:56536122..56568603,201	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000257809	TF binding region
ENSG00000257809	CpG island
ENSG00000258345	Chromatin interaction
ENSG00000258317	Chromatin interaction
ENSG00000258199	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000139613	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000139641	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12227040	1.00[MEX][hapmap]
rs2855320	1.00[MEX][hapmap]
rs35807059	1.00[MEX][hapmap]
rs7962107	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv559013	chr12:56551249-56556389	Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 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	chr12:56553000-56557000	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
2	chr12:56553200-56556800	Transcr. at gene 5' and 3'	Colon Smooth Muscle	Colon
3	chr12:56553200-56557800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr12:56554000-56557400	Genic enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:56554000-56582000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr12:56554200-56556600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
7	chr12:56554200-56581400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr12:56554600-56556800	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr12:56554600-56557400	Genic enhancers	HUES48 Cell Line	embryonic stem cell
10	chr12:56554600-56557600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:56554600-56558200	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:56554600-56568600	Strong transcription	Ovary	ovary
13	chr12:56554800-56556600	Genic enhancers	Primary neutrophils fromperipheralblood	blood
14	chr12:56554800-56556600	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr12:56554800-56557600	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr12:56555000-56556400	Strong transcription	HSMMtube	muscle
17	chr12:56555000-56556600	Genic enhancers	Primary T cells fromperipheralblood	blood
18	chr12:56555000-56556600	Strong transcription	Psoas Muscle	Psoas
19	chr12:56555000-56556800	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr12:56555000-56556800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
21	chr12:56555000-56556800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
22	chr12:56555000-56557200	Genic enhancers	HUES64 Cell Line	embryonic stem cell
23	chr12:56555000-56557400	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr12:56555000-56557600	Genic enhancers	Fetal Muscle Leg	muscle
25	chr12:56555000-56557800	Genic enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr12:56555000-56558400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr12:56555000-56569600	Strong transcription	Brain Substantia Nigra	brain
28	chr12:56555000-56575600	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr12:56555000-56579800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr12:56555000-56580800	Strong transcription	H9 Cell Line	embryonic stem cell
31	chr12:56555000-56580800	Strong transcription	Brain Anterior Caudate	brain
32	chr12:56555000-56581000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr12:56555200-56556400	Strong transcription	H1 Cell Line	embryonic stem cell
34	chr12:56555200-56556400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr12:56555200-56557400	Genic enhancers	Brain Germinal Matrix	brain
36	chr12:56555200-56559600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr12:56555200-56559600	Strong transcription	Small Intestine	intestine
38	chr12:56555200-56560600	Strong transcription	Lung	lung
39	chr12:56555200-56562000	Strong transcription	Primary B cells from cord blood	blood
40	chr12:56555200-56563200	Weak transcription	Right Atrium	heart
41	chr12:56555200-56565200	Weak transcription	Fetal Brain Male	brain
42	chr12:56555200-56573600	Strong transcription	Fetal Lung	lung
43	chr12:56555200-56578800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr12:56555200-56580600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr12:56555200-56580800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr12:56555400-56556400	Strong transcription	A549	lung
47	chr12:56555400-56556600	Genic enhancers	Colonic Mucosa	Colon
48	chr12:56555400-56556600	Genic enhancers	Fetal Stomach	stomach
49	chr12:56555400-56556600	Genic enhancers	Dnd41	blood
50	chr12:56555400-56556600	Genic enhancers	NHDF-Ad	bronchial

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