Variant report

Variant	rs12308277
Chromosome Location	chr12:56216070-56216071
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:75)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:75 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:56216060-56216210	SAEC	small airway:	n/a	n/a
2	RAD21	chr12:56216011-56216267	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTCF	chr12:56216034-56216291	HepG2	liver:	n/a	n/a
4	CTCF	chr12:56216020-56216170	BE2_C	brain:	n/a	n/a
5	TEAD4	chr12:56215996-56216397	HCT-116	colon:	n/a	n/a
6	POLR2A	chr12:56215977-56216575	SK-N-SH	brain:	n/a	n/a
7	CTCF	chr12:56216060-56216210	GM12872	blood:	n/a	n/a
8	CTCF	chr12:56216040-56216190	GM12865	blood:	n/a	n/a
9	TEAD4	chr12:56215905-56216398	A549	lung:	n/a	n/a
10	CTCF	chr12:56216060-56216210	AG04449	skin:	n/a	n/a
11	POLR2A	chr12:56216051-56217285	PFSK-1	brain:	n/a	n/a
12	TEAD4	chr12:56215888-56216482	ECC-1	luminal epithelium:	n/a	n/a
13	CTCF	chr12:56215735-56216526	A549	lung:	n/a	n/a
14	TEAD4	chr12:56215902-56216413	ECC-1	luminal epithelium:	n/a	n/a
15	POLR2A	chr12:56215620-56216299	K562	blood:	n/a	n/a
16	TEAD4	chr12:56215929-56216385	K562	blood:	n/a	n/a
17	TEAD4	chr12:56215896-56216423	HepG2	liver:	n/a	n/a
18	CTCF	chr12:56215898-56216502	HCT-116	colon:	n/a	n/a
19	CTCF	chr12:56216062-56216287	HepG2	liver:	n/a	n/a
20	CTCF	chr12:56216040-56216190	GM12873	blood:	n/a	n/a
21	CTCF	chr12:56216060-56216210	AG10803	skin:	n/a	n/a
22	POLR2A	chr12:56215985-56216395	HCT-116	colon:	n/a	n/a
23	CTCF	chr12:56216067-56216282	MCF-7	breast:	n/a	n/a
24	POLR2A	chr12:56216009-56216664	MCF-7	breast:	n/a	n/a
25	CTCF	chr12:56216000-56216150	AG04450	lung:	n/a	n/a
26	CTCF	chr12:56215961-56216296	A549	lung:	n/a	n/a
27	RAD21	chr12:56216039-56216331	HepG2	liver:	n/a	n/a
28	CTCF	chr12:56215923-56216371	A549	lung:	n/a	n/a
29	POLR2A	chr12:56215840-56216612	Hela-S3	cervix:	n/a	n/a
30	CTCF	chr12:56216060-56216210	HVMF	connective:	n/a	n/a
31	CTCF	chr12:56216040-56216190	HRE	kidney:	n/a	n/a
32	POLR2A	chr12:56215047-56216666	SK-N-MC	brain:	n/a	n/a
33	CTCF	chr12:56216000-56216150	NHDF-neo	bronchial:	n/a	n/a
34	POLR2A	chr12:56215826-56216563	GM12891	blood:	n/a	n/a
35	CTCF	chr12:56216000-56216150	HAc	cerebellar:	n/a	n/a
36	CTCF	chr12:56216060-56216210	AoAF	blood vessel:	n/a	n/a
37	SMC3	chr12:56216017-56216329	Hela-S3	cervix:	n/a	n/a
38	ARID3A	chr12:56216019-56216325	HepG2	liver:	n/a	n/a
39	TEAD4	chr12:56215966-56216428	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr12:56210869-56217420	PANC-1	pancreas:	n/a	n/a
41	TEAD4	chr12:56215927-56216565	A549	lung:	n/a	n/a
42	CTCF	chr12:56216017-56216261	H1-hESC	embryonic stem cell:	n/a	n/a
43	CTCF	chr12:56216020-56216170	RPTEC	kidney:	n/a	n/a
44	POLR2A	chr12:56215019-56216619	K562	blood:	n/a	n/a
45	CTCF	chr12:56216020-56216170	SK-N-SH_RA	brain:	n/a	n/a
46	CTCF	chr12:56216040-56216190	HCT-116	colon:	n/a	n/a
47	CTCF	chr12:56216000-56216150	NHEK	skin:	n/a	n/a
48	POLR2A	chr12:56215974-56216681	HepG2	liver:	n/a	n/a
49	POLR2A	chr12:56215806-56217331	K562	blood:	n/a	n/a
50	FOXA1	chr12:56215980-56216366	HepG2	liver:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56208117..56217611-chr12:56318345..56328982,45	MCF-7	breast:
2	chr12:56215501..56218229-chr12:56435241..56437091,2	MCF-7	breast:
3	chr12:56122044..56125126-chr12:56213090..56216394,4	MCF-7	breast:
4	chr12:56212373..56216209-chr12:56435568..56437517,3	MCF-7	breast:
5	chr12:56210044..56216553-chr12:56364276..56371676,13	MCF-7	breast:
6	chr12:56136775..56139143-chr12:56214826..56217314,2	MCF-7	breast:
7	chr12:56208546..56216914-chr12:56318326..56328671,24	MCF-7	breast:
8	chr12:56211687..56216264-chr12:56332406..56336008,6	MCF-7	breast:

No data

Variant related genes	Relation type
SARNP	TF binding region
ENSG00000065357	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000135404	Chromatin interaction
ENSG00000170473	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000258056	Chromatin interaction
ENSG00000123374	Chromatin interaction
ENSG00000135414	Chromatin interaction
ENSG00000111540	Chromatin interaction
ENSG00000185664	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs12320132	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1463591	0.84[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17118032	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3802998	1.00[CHB][hapmap]
rs56699787	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58599597	0.95[ASN][1000 genomes]
rs59980563	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs68101940	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7310164	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73119263	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7959622	1.00[GIH][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832423	chr12:56080822-56253698	Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56212800-56217800	Strong transcription	HUES6 Cell Line	embryonic stem cell
2	chr12:56212800-56218200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:56213000-56216200	Weak transcription	Fetal Brain Male	brain
4	chr12:56213000-56216800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr12:56213000-56217000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:56213000-56217200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
7	chr12:56213000-56217200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr12:56213000-56217200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr12:56213000-56217200	Strong transcription	Brain Substantia Nigra	brain
10	chr12:56213000-56217200	Strong transcription	Stomach Smooth Muscle	stomach
11	chr12:56213000-56217400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
12	chr12:56213000-56217400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr12:56213000-56217400	Strong transcription	Cortex derived primary cultured neurospheres	brain
14	chr12:56213000-56217400	Strong transcription	Colon Smooth Muscle	Colon
15	chr12:56213000-56217400	Strong transcription	Placenta	Placenta
16	chr12:56213000-56217400	Strong transcription	Skeletal Muscle Male	skeletal muscle
17	chr12:56213000-56217600	Strong transcription	Fetal Lung	lung
18	chr12:56213000-56217600	Strong transcription	Fetal Stomach	stomach
19	chr12:56213000-56217600	Strong transcription	HSMMtube	muscle
20	chr12:56213000-56217800	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr12:56213000-56217800	Weak transcription	Fetal Kidney	kidney
22	chr12:56213000-56218000	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr12:56213000-56218000	Strong transcription	Skeletal Muscle Female	skeletal muscle
24	chr12:56213000-56218400	Strong transcription	Fetal Muscle Trunk	muscle
25	chr12:56213000-56218600	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr12:56213000-56220400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr12:56213000-56221000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr12:56213200-56217000	Strong transcription	Primary hematopoietic stem cells	blood
29	chr12:56213200-56217000	Strong transcription	Rectal Smooth Muscle	rectum
30	chr12:56213200-56217200	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr12:56213200-56217200	Strong transcription	Left Ventricle	heart
32	chr12:56213200-56217200	Strong transcription	Lung	lung
33	chr12:56213200-56217200	Strong transcription	HUVEC	blood vessel
34	chr12:56213200-56217400	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr12:56213200-56217400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr12:56213200-56217400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr12:56213200-56217400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr12:56213200-56217400	Strong transcription	Colonic Mucosa	Colon
39	chr12:56213200-56217400	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr12:56213200-56217400	Strong transcription	Spleen	Spleen
41	chr12:56213200-56217600	Strong transcription	K562	blood
42	chr12:56213200-56217600	Strong transcription	Osteobl	bone
43	chr12:56213200-56217800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr12:56213200-56218000	Strong transcription	Primary B cells from cord blood	blood
45	chr12:56213200-56218000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr12:56213200-56218000	Strong transcription	Adipose Nuclei	Adipose
47	chr12:56213200-56218200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr12:56213200-56218200	Strong transcription	Brain Anterior Caudate	brain
49	chr12:56213200-56218200	Strong transcription	Brain Germinal Matrix	brain
50	chr12:56213200-56218200	Strong transcription	Fetal Brain Female	brain

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