Variant report

Variant	rs34299538
Chromosome Location	chr12:58088085-58088086
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	MAX	chr12:58087380-58088169	K562	blood:	n/a	n/a
2	SP1	chr12:58087433-58088132	GM12878	blood:	n/a	n/a
3	GABPA	chr12:58087438-58088302	SK-N-SH	brain:	n/a	n/a
4	IRF1	chr12:58087376-58088148	K562	blood:	n/a	chr12:58087850-58087859 chr12:58087724-58087733
5	MAZ	chr12:58087519-58088154	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr12:58087728-58088156	H1-hESC	embryonic stem cell:	n/a	n/a
7	TCF7L2	chr12:58087471-58088098	HEK293	kidney:	n/a	chr12:58087651-58087665
8	ELF1	chr12:58087369-58088339	GM12878	blood:	n/a	chr12:58088159-58088170 chr12:58088139-58088150
9	SP1	chr12:58087315-58088161	K562	blood:	n/a	n/a
10	MAX	chr12:58087407-58088128	Hela-S3	cervix:	n/a	n/a
11	MXI1	chr12:58087396-58088351	GM12878	blood:	n/a	n/a
12	TAF1	chr12:58087805-58088167	HepG2	liver:	n/a	n/a
13	YY1	chr12:58087731-58088167	GM12891	blood:	n/a	chr12:58087940-58087952
14	STAT3	chr12:58087382-58088301	GM12878	blood:	n/a	n/a
15	TCF12	chr12:58087300-58088365	ECC-1	luminal epithelium:	n/a	chr12:58088278-58088286
16	BHLHE40	chr12:58087403-58088305	GM12878	blood:	n/a	n/a
17	ZNF143	chr12:58087314-58088142	H1-hESC	embryonic stem cell:	n/a	chr12:58087570-58087580
18	REST	chr12:58087722-58088316	ECC-1	luminal epithelium:	n/a	chr12:58087789-58087803
19	POLR2A	chr12:58087497-58088172	IMR90	lung:	n/a	n/a
20	POLR2A	chr12:58087708-58088159	PANC-1	pancreas:	n/a	n/a
21	TBP	chr12:58087394-58088141	Hela-S3	cervix:	n/a	n/a
22	HEY1	chr12:58087747-58088195	HepG2	liver:	n/a	n/a
23	STAT1	chr12:58087519-58088113	GM12878	blood:	n/a	n/a
24	CHD2	chr12:58087455-58088428	Hela-S3	cervix:	n/a	n/a
25	ZNF143	chr12:58087372-58088309	GM12878	blood:	n/a	chr12:58087570-58087580
26	POLR2A	chr12:58087537-58088452	GM18526	blood:	n/a	n/a
27	TAF1	chr12:58087700-58088157	GM12878	blood:	n/a	n/a
28	SPI1	chr12:58088037-58088256	K562	blood:	n/a	chr12:58088162-58088169 chr12:58088142-58088149 chr12:58088141-58088150
29	SIN3AK20	chr12:58087449-58088339	K562	blood:	n/a	n/a
30	POLR2A	chr12:58087789-58088103	HepG2	liver:	n/a	n/a
31	POLR2A	chr12:58087366-58088170	SK-N-SH	brain:	n/a	n/a
32	REST	chr12:58087743-58088250	PFSK-1	brain:	n/a	chr12:58087789-58087803
33	POLR2A	chr12:58087530-58088198	GM12878	blood:	n/a	n/a
34	PML	chr12:58087103-58088359	GM12878	blood:	n/a	n/a
35	YY1	chr12:58087440-58088438	GM12878	blood:	n/a	chr12:58087940-58087952
36	SP1	chr12:58087306-58088298	A549	lung:	n/a	n/a
37	MAFK	chr12:58087416-58088151	K562	blood:	n/a	n/a
38	FOXA2	chr12:58087457-58088160	A549	lung:	n/a	n/a
39	POLR2A	chr12:58087805-58088176	GM12891	blood:	n/a	n/a
40	POLR2A	chr12:58087727-58088231	Hela-S3	cervix:	n/a	n/a
41	HDAC2	chr12:58087766-58088135	HepG2	liver:	n/a	n/a
42	ELF1	chr12:58087450-58088330	K562	blood:	n/a	chr12:58088159-58088170 chr12:58088139-58088150
43	NFIC	chr12:58087466-58088105	HepG2	liver:	n/a	n/a
44	TAF1	chr12:58087686-58088116	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr12:58087528-58088542	H1-hESC	embryonic stem cell:	n/a	n/a
46	ATF2	chr12:58087432-58088158	GM12878	blood:	n/a	n/a
47	HEY1	chr12:58087778-58088118	HepG2	liver:	n/a	n/a
48	REST	chr12:58087889-58088105	HepG2	liver:	n/a	n/a
49	YY1	chr12:58087441-58088376	GM12878	blood:	n/a	chr12:58087940-58087952
50	KAP1	chr12:58086992-58088113	HEK293	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:57915543..57917497-chr12:58086337..58088295,2	K562	blood:
2	chr12:58086909..58089805-chr12:58175888..58177930,2	K562	blood:
3	chr12:57983103..57986007-chr12:58086180..58089172,2	MCF-7	breast:
4	chr12:58086950..58089833-chr12:58113163..58115231,2	K562	blood:
5	chr12:58085407..58089363-chr12:58117669..58123604,12	MCF-7	breast:
6	chr12:58087963..58090015-chr12:58135422..58139186,3	K562	blood:
7	chr12:57907013..57909948-chr12:58087318..58089281,2	K562	blood:
8	chr12:58007718..58010411-chr12:58087376..58090012,2	MCF-7	breast:
9	chr12:58086741..58089162-chr12:58114553..58116663,2	MCF-7	breast:
10	chr12:57910924..57913637-chr12:58087334..58089189,3	K562	blood:
11	chr12:58087206..58088752-chr12:58165817..58167834,2	MCF-7	breast:
12	chr12:58062107..58064323-chr12:58086416..58089211,2	K562	blood:
13	chr12:58085694..58088995-chr12:58116929..58123534,7	MCF-7	breast:
14	chr12:57913089..57916136-chr12:58086816..58089656,3	MCF-7	breast:
15	chr12:57983190..57986031-chr12:58086563..58089648,3	K562	blood:

Variant related genes	Relation type
OS9	TF binding region
ENSG00000257499	Chromatin interaction
ENSG00000240771	Chromatin interaction
ENSG00000238436	Chromatin interaction
ENSG00000123427	Chromatin interaction
ENSG00000037897	Chromatin interaction
ENSG00000135506	Chromatin interaction
ENSG00000264046	Chromatin interaction
ENSG00000175197	Chromatin interaction
ENSG00000166908	Chromatin interaction
ENSG00000208028	Chromatin interaction
ENSG00000255737	Chromatin interaction
ENSG00000257921	Chromatin interaction
ENSG00000123297	Chromatin interaction
ENSG00000224713	Chromatin interaction
ENSG00000257342	Chromatin interaction
ENSG00000166987	Chromatin interaction
ENSG00000135452	Chromatin interaction
ENSG00000166986	Chromatin interaction
ENSG00000135439	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs55849950	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56318011	1.00[AMR][1000 genomes]
rs58824032	1.00[AMR][1000 genomes]
rs59476756	1.00[AMR][1000 genomes]
rs73334082	1.00[AMR][1000 genomes]
rs73335910	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73338222	1.00[AMR][1000 genomes]
rs73338246	1.00[AMR][1000 genomes]
rs73338249	1.00[AMR][1000 genomes]
rs73338250	1.00[AMR][1000 genomes]
rs73338252	1.00[AMR][1000 genomes]
rs73349954	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74094487	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv508676	chr12:58045136-58098538	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases
4	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58087000-58088200	Active TSS	Stomach Smooth Muscle	stomach
2	chr12:58087000-58088400	Active TSS	Brain Cingulate Gyrus	brain
3	chr12:58087000-58088600	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr12:58087000-58089000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr12:58087200-58088200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
6	chr12:58087200-58088200	Active TSS	Placenta	Placenta
7	chr12:58087200-58088400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr12:58087200-58088400	Active TSS	Brain Angular Gyrus	brain
9	chr12:58087200-58088400	Active TSS	Brain Hippocampus Middle	brain
10	chr12:58087200-58088400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr12:58087200-58088400	Active TSS	Colon Smooth Muscle	Colon
12	chr12:58087200-58088400	Active TSS	Psoas Muscle	Psoas
13	chr12:58087200-58088400	Active TSS	HSMMtube	muscle
14	chr12:58087200-58088400	Active TSS	Osteobl	bone
15	chr12:58087200-58088600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr12:58087200-58088600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr12:58087200-58088600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr12:58087200-58088600	Active TSS	Brain Anterior Caudate	brain
19	chr12:58087200-58088600	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr12:58087200-58088600	Active TSS	Pancreas	Pancrea
21	chr12:58087200-58088600	Active TSS	A549	lung
22	chr12:58087200-58088600	Active TSS	NHLF	lung
23	chr12:58087200-58088800	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr12:58087200-58088800	Active TSS	Colonic Mucosa	Colon
25	chr12:58087200-58088800	Active TSS	GM12878-XiMat	blood
26	chr12:58087200-58089000	Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr12:58087200-58089000	Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr12:58087200-58089000	Active TSS	iPS-20b Cell Line	embryonic stem cell
29	chr12:58087400-58088200	Active TSS	Primary B cells from cord blood	blood
30	chr12:58087400-58088200	Active TSS	Primary T cells fromperipheralblood	blood
31	chr12:58087400-58088200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
32	chr12:58087400-58088200	Active TSS	Liver	Liver
33	chr12:58087400-58088200	Active TSS	Fetal Muscle Trunk	muscle
34	chr12:58087400-58088400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr12:58087400-58088400	Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr12:58087400-58088400	Active TSS	Primary T cells from cord blood	blood
37	chr12:58087400-58088400	Active TSS	Primary hematopoietic stem cells	blood
38	chr12:58087400-58088400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
39	chr12:58087400-58088400	Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr12:58087400-58088400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
41	chr12:58087400-58088400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr12:58087400-58088400	Active TSS	Muscle Satellite Cultured Cells	--
43	chr12:58087400-58088400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr12:58087400-58088400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr12:58087400-58088400	Active TSS	Brain Inferior Temporal Lobe	brain
46	chr12:58087400-58088400	Active TSS	Brain Substantia Nigra	brain
47	chr12:58087400-58088400	Active TSS	Duodenum Smooth Muscle	Duodenum
48	chr12:58087400-58088400	Active TSS	Fetal Lung	lung
49	chr12:58087400-58088400	Active TSS	Fetal Stomach	stomach
50	chr12:58087400-58088400	Active TSS	Fetal Thymus	thymus

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