Variant report

Variant	rs12423796
Chromosome Location	chr12:117515569-117515570
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:117513474..117515801-chr12:117535045..117537762,2	K562	blood:

Variant related genes	Relation type
ENSG00000258285	Chromatin interaction
ENSG00000088992	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10744889	0.92[ASW][hapmap];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];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10744890	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10774901	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10850754	0.92[ASW][hapmap];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];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1106277	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1546246	0.85[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1546247	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1546248	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2173651	0.85[CEU][hapmap];0.86[CHB][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4341616	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7304889	1.00[CEU][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7308236	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7959367	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7963451	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7964686	0.83[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	nsv519118	chr12:117386085-117521180	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv1804583	chr12:117472107-117525169	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12423796	TESC	cis	parietal	SCAN
rs12423796	BRAP	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117499000-117522000	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr12:117501400-117518600	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr12:117508200-117523200	Weak transcription	Brain Hippocampus Middle	brain
4	chr12:117508600-117520200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr12:117509800-117521000	Weak transcription	A549	lung
6	chr12:117510800-117518600	Weak transcription	Thymus	Thymus
7	chr12:117514200-117515600	Enhancers	Right Ventricle	heart
8	chr12:117514400-117515600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr12:117514600-117515600	Genic enhancers	HepG2	liver
10	chr12:117514600-117515800	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr12:117515000-117518400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr12:117515000-117518400	Weak transcription	Primary hematopoietic stem cells	blood
13	chr12:117515000-117524800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr12:117515200-117518200	Weak transcription	Fetal Thymus	thymus
15	chr12:117515200-117518600	Weak transcription	Left Ventricle	heart
16	chr12:117515200-117518800	Weak transcription	Fetal Kidney	kidney
17	chr12:117515200-117521200	Weak transcription	Fetal Lung	lung
18	chr12:117515200-117521400	Weak transcription	Stomach Mucosa	stomach
19	chr12:117515200-117522400	Weak transcription	Brain Anterior Caudate	brain
20	chr12:117515200-117535200	Weak transcription	Primary T cells from cord blood	blood
21	chr12:117515400-117516000	Enhancers	Dnd41	blood
22	chr12:117515400-117518200	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr12:117515400-117518200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr12:117515400-117518200	Weak transcription	Fetal Heart	heart
25	chr12:117515400-117518600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr12:117515400-117520800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr12:117515400-117520800	Weak transcription	Pancreas	Pancrea
28	chr12:117515400-117520800	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr12:117515400-117523000	Weak transcription	Gastric	stomach
30	chr12:117515400-117526400	Weak transcription	Spleen	Spleen
31	chr12:117515400-117528600	Weak transcription	K562	blood

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