Variant report

Variant	rs12423097
Chromosome Location	chr12:4872772-4872773
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	CTCF	chr12:4872760-4873103	K562	blood:	n/a	n/a
2	CTCF	chr12:4872761-4873062	K562	blood:	n/a	n/a
3	GABPA	chr12:4872640-4873097	K562	blood:	n/a	chr12:4872798-4872807
4	CTCF	chr12:4872764-4873117	K562	blood:	n/a	n/a
5	ZNF143	chr12:4872737-4873180	H1-hESC	embryonic stem cell:	n/a	n/a
6	EP300	chr12:4872728-4873082	H1-hESC	embryonic stem cell:	n/a	chr12:4872732-4872746
7	CTCF	chr12:4872677-4873168	H1-hESC	embryonic stem cell:	n/a	n/a
8	YY1	chr12:4872755-4873122	H1-hESC	embryonic stem cell:	n/a	chr12:4872798-4872807 chr12:4872790-4872801 chr12:4872790-4872799
9	YY1	chr12:4872704-4873244	H1-hESC	embryonic stem cell:	n/a	chr12:4872798-4872807 chr12:4872790-4872801 chr12:4872790-4872799
10	YY1	chr12:4872760-4873054	HepG2	liver:	n/a	chr12:4872798-4872807 chr12:4872790-4872801 chr12:4872790-4872799
11	JUND	chr12:4872758-4873113	H1-hESC	embryonic stem cell:	n/a	chr12:4872794-4872803 chr12:4872790-4872799
12	RCOR1	chr12:4872729-4873071	K562	blood:	n/a	n/a
13	NANOG	chr12:4872738-4873002	H1-hESC	embryonic stem cell:	n/a	n/a
14	MAZ	chr12:4872729-4873099	K562	blood:	n/a	n/a
15	CTCF	chr12:4872609-4873338	A549	lung:	n/a	n/a
16	TCF12	chr12:4872772-4873030	H1-hESC	embryonic stem cell:	n/a	n/a
17	RAD21	chr12:4872741-4873133	H1-hESC	embryonic stem cell:	n/a	chr12:4872984-4872996
18	RAD21	chr12:4872692-4873151	H1-hESC	embryonic stem cell:	n/a	chr12:4872984-4872996
19	ELF1	chr12:4872750-4873032	K562	blood:	n/a	n/a
20	MAZ	chr12:4872754-4873023	HepG2	liver:	n/a	n/a
21	EGR1	chr12:4872670-4872910	K562	blood:	n/a	chr12:4872800-4872809 chr12:4872799-4872812 chr12:4872799-4872812 chr12:4872797-4872807
22	RAD21	chr12:4872653-4873173	H1-hESC	embryonic stem cell:	n/a	chr12:4872984-4872996
23	SP1	chr12:4872619-4873169	H1-hESC	embryonic stem cell:	n/a	chr12:4872793-4872802 chr12:4872797-4872807 chr12:4872791-4872803 chr12:4872797-4872806 chr12:4872796-4872808 chr12:4872792-4872801 chr12:4872797-4872807 chr12:4872796-4872808 chr12:4872792-4872806 chr12:4872798-4872807 chr12:4872797-4872806 chr12:4872791-4872803
24	CTCF	chr12:4872733-4873155	H1-hESC	embryonic stem cell:	n/a	n/a
25	MYC	chr12:4872747-4873147	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
GALNT8	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10492056	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11063326	0.82[CHB][hapmap];0.80[CHD][hapmap];0.90[JPT][hapmap]
rs17176851	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17177150	0.93[EUR][1000 genomes]
rs17177163	0.93[EUR][1000 genomes]
rs17783505	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2058209	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4765785	0.93[EUR][1000 genomes]

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	nsv832318	chr12:4655799-4875837	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1054218	chr12:4819576-4882667	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4854200-4876000	Weak transcription	Fetal Brain Male	brain
2	chr12:4867200-4880200	Weak transcription	Spleen	Spleen
3	chr12:4868200-4874400	Weak transcription	Left Ventricle	heart
4	chr12:4868800-4874600	Weak transcription	Right Ventricle	heart
5	chr12:4869000-4875400	Weak transcription	Fetal Stomach	stomach
6	chr12:4869600-4873600	Strong transcription	Brain Germinal Matrix	brain
7	chr12:4869600-4875600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr12:4869800-4884200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr12:4871200-4874400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:4871800-4877800	Weak transcription	Brain Hippocampus Middle	brain
11	chr12:4872000-4875200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr12:4872200-4873200	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr12:4872200-4873400	Active TSS	Brain Substantia Nigra	brain
14	chr12:4872200-4873600	Active TSS	K562	blood
15	chr12:4872400-4872800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr12:4872400-4873200	Enhancers	HUES48 Cell Line	embryonic stem cell
17	chr12:4872400-4873200	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr12:4872400-4873200	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr12:4872400-4873200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr12:4872400-4873200	Active TSS	Stomach Smooth Muscle	stomach
21	chr12:4872400-4873400	Enhancers	H1 Cell Line	embryonic stem cell
22	chr12:4872400-4873400	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr12:4872600-4873200	Flanking Active TSS	Ovary	ovary
24	chr12:4872600-4873200	Flanking Active TSS	HepG2	liver
25	chr12:4872600-4873400	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr12:4872600-4873400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr12:4872600-4873400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr12:4872600-4874600	Strong transcription	Fetal Brain Female	brain

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