Variant report

Variant	rs7302975
Chromosome Location	chr12:32138924-32138925
allele	C/T
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	chr12:32138716-32139198	GM12878	blood:	n/a	n/a
2	FOXA1	chr12:32138749-32139245	HepG2	liver:	n/a	chr12:32139055-32139067 chr12:32139016-32139028
3	FOXA1	chr12:32138770-32139212	HepG2	liver:	n/a	chr12:32139055-32139067 chr12:32139016-32139028
4	POLR2A	chr12:32138836-32139017	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr12:32138765-32139195	GM12892	blood:	n/a	n/a
6	POLR2A	chr12:32138858-32139036	K562	blood:	n/a	n/a
7	POLR2A	chr12:32133625-32140479	K562	blood:	n/a	n/a
8	POLR2A	chr12:32138641-32139151	H1-hESC	embryonic stem cell:	n/a	n/a
9	FOXA1	chr12:32138863-32139128	T-47D	breast:	n/a	chr12:32139055-32139067 chr12:32139016-32139028
10	POLR2A	chr12:32138730-32139207	GM12892	blood:	n/a	n/a
11	FOXA2	chr12:32138831-32139154	HepG2	liver:	n/a	chr12:32139055-32139067 chr12:32139016-32139028
12	FOXA1	chr12:32138796-32139195	HepG2	liver:	n/a	chr12:32139055-32139067 chr12:32139016-32139028
13	POLR2A	chr12:32138653-32139126	PANC-1	pancreas:	n/a	n/a
14	POLR2A	chr12:32133922-32140576	GM12878	blood:	n/a	n/a
15	FOXA1	chr12:32138752-32139181	HepG2	liver:	n/a	chr12:32139055-32139067 chr12:32139016-32139028

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:32134776..32136831-chr12:32137992..32139591,2	MCF-7	breast:

Variant related genes	Relation type
KIAA1551	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10743773	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10771895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2166807	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2388982	0.82[CHB][hapmap];0.83[CHD][hapmap];0.82[MEX][hapmap]
rs3759301	0.84[JPT][hapmap]
rs4930999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4931000	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4931002	0.95[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4931004	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4931005	0.83[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6488023	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043010	chr12:31798446-32143151	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv541446	chr12:31798446-32143151	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv558100	chr12:31866833-32185924	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1045464	chr12:31869888-32183792	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv541447	chr12:31869888-32183792	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
6	esv3363806	chr12:31872264-32410283	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
7	esv3508621	chr12:31872654-32410593	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
8	esv3508622	chr12:31872654-32410593	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7302975	C12orf72	cis	cerebellum	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32114000-32150800	Weak transcription	NHLF	lung
2	chr12:32116000-32141800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
3	chr12:32116400-32143200	ZNF genes & repeats	GM12878-XiMat	blood
4	chr12:32120600-32141600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr12:32120800-32140400	ZNF genes & repeats	Primary T cells from cord blood	blood
6	chr12:32121200-32139000	ZNF genes & repeats	Fetal Brain Female	brain
7	chr12:32121800-32141600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
8	chr12:32122600-32139000	ZNF genes & repeats	Primary B cells from cord blood	blood
9	chr12:32123200-32139600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
10	chr12:32123200-32143800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
11	chr12:32123400-32143200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
12	chr12:32123800-32143200	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
13	chr12:32124600-32140000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
14	chr12:32128800-32139800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
15	chr12:32128800-32150600	Weak transcription	Hela-S3	cervix
16	chr12:32129400-32139000	ZNF genes & repeats	Fetal Muscle Leg	muscle
17	chr12:32130400-32150200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr12:32131600-32139800	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
19	chr12:32132000-32139000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr12:32132000-32139200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
21	chr12:32132000-32139800	ZNF genes & repeats	K562	blood
22	chr12:32132200-32139200	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
23	chr12:32132200-32139400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
24	chr12:32132200-32139800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
25	chr12:32132800-32147200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr12:32133600-32142000	ZNF genes & repeats	Brain Germinal Matrix	brain
27	chr12:32134800-32142400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr12:32134800-32149400	Weak transcription	Esophagus	oesophagus
29	chr12:32134800-32149800	Weak transcription	Pancreas	Pancrea
30	chr12:32134800-32151000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr12:32134800-32155400	Weak transcription	NHDF-Ad	bronchial
32	chr12:32135000-32141600	Weak transcription	Lung	lung
33	chr12:32135000-32142400	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr12:32135000-32143000	Weak transcription	Spleen	Spleen
35	chr12:32135000-32147800	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr12:32135000-32148600	Weak transcription	Brain Hippocampus Middle	brain
37	chr12:32135000-32149200	Weak transcription	Brain Substantia Nigra	brain
38	chr12:32135000-32149800	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr12:32135000-32149800	Weak transcription	Colon Smooth Muscle	Colon
40	chr12:32135000-32150000	Weak transcription	Right Ventricle	heart
41	chr12:32135000-32150200	Weak transcription	Rectal Smooth Muscle	rectum
42	chr12:32135000-32150800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr12:32135000-32156000	Weak transcription	Brain Cingulate Gyrus	brain
44	chr12:32135000-32156400	Weak transcription	Gastric	stomach
45	chr12:32135200-32141400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr12:32135200-32148200	Weak transcription	Brain Angular Gyrus	brain
47	chr12:32135400-32141400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr12:32135400-32142400	Weak transcription	NHEK	skin
49	chr12:32135600-32140800	Weak transcription	Fetal Stomach	stomach
50	chr12:32135600-32148800	Weak transcription	Stomach Smooth Muscle	stomach

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