Variant report

Variant	rs2249454
Chromosome Location	chr12:105324121-105324122
allele	A/C
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	STAT5A	chr12:105324120-105325041	GM12878	blood:	n/a	n/a
2	NFIC	chr12:105323618-105325783	GM12878	blood:	n/a	n/a
3	PML	chr12:105324080-105324947	GM12878	blood:	n/a	n/a
4	NFIC	chr12:105323882-105325007	GM12878	blood:	n/a	n/a
5	MTA3	chr12:105323998-105324884	GM12878	blood:	n/a	n/a
6	YY1	chr12:105324040-105324845	GM12878	blood:	n/a	n/a
7	MTA3	chr12:105323932-105325671	GM12878	blood:	n/a	n/a
8	TBL1XR1	chr12:105323864-105324953	GM12878	blood:	n/a	n/a
9	RELA	chr12:105324047-105324966	GM19099	blood:	n/a	n/a
10	RELA	chr12:105323874-105324949	GM12891	blood:	n/a	n/a
11	RELA	chr12:105324041-105324903	GM10847	blood:	n/a	n/a
12	RCOR1	chr12:105324116-105324829	GM12878	blood:	n/a	n/a
13	RUNX3	chr12:105324084-105325160	GM12878	blood:	n/a	n/a
14	FOXM1	chr12:105323864-105324870	GM12878	blood:	n/a	chr12:105324215-105324223
15	WRNIP1	chr12:105324021-105324221	GM12878	blood:	n/a	n/a
16	POLR2A	chr12:105323973-105324298	GM12878	blood:	n/a	n/a
17	BATF	chr12:105324047-105325069	GM12878	blood:	n/a	n/a
18	EBF1	chr12:105324086-105325154	GM12878	blood:	n/a	n/a
19	RELA	chr12:105323970-105324923	GM12878	blood:	n/a	n/a
20	IKZF1	chr12:105323729-105325352	GM12878	blood:	n/a	chr12:105323831-105323843
21	TBP	chr12:105324045-105325167	GM12878	blood:	n/a	n/a
22	ATF2	chr12:105323814-105325034	GM12878	blood:	n/a	n/a
23	STAT1	chr12:105324052-105324740	GM12878	blood:	n/a	n/a
24	RELA	chr12:105324021-105324864	GM12892	blood:	n/a	n/a
25	CHD2	chr12:105324118-105324811	GM12878	blood:	n/a	n/a
26	RELA	chr12:105323847-105324984	GM18505	blood:	n/a	n/a
27	RELA	chr12:105324076-105324980	GM18951	blood:	n/a	n/a
28	EP300	chr12:105324115-105324874	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
SLC41A2	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1002803	0.86[CHD][hapmap];0.83[GIH][hapmap]
rs10507184	0.86[ASW][hapmap];0.84[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap]
rs10746008	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10778355	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10778358	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10861294	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10861296	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11112253	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11610388	0.84[ASN][1000 genomes]
rs1389612	0.84[CHB][hapmap];0.81[JPT][hapmap]
rs1565813	0.86[ASW][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap]
rs2248012	0.90[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap]
rs2248986	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2264892	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2453155	0.81[GIH][hapmap]
rs2453156	0.84[CHB][hapmap]
rs2453161	0.83[CHD][hapmap]
rs2453166	0.86[ASW][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap]
rs2463018	0.84[CHB][hapmap];0.83[CHD][hapmap];0.83[GIH][hapmap]
rs2463440	0.86[CHD][hapmap]
rs2463441	0.83[CHD][hapmap]
rs2468089	0.80[GIH][hapmap]
rs2468092	0.81[JPT][hapmap]
rs2468105	0.84[CHB][hapmap];0.85[JPT][hapmap]
rs2468109	0.83[CHD][hapmap]
rs2468337	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2730291	0.86[CHD][hapmap];0.83[GIH][hapmap]
rs4076550	0.86[CEU][hapmap]
rs4334113	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4388976	0.90[CHB][hapmap];0.93[JPT][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4393404	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4964310	0.84[CHB][hapmap];0.94[JPT][hapmap]
rs4964316	0.80[GIH][hapmap]
rs6539170	0.86[ASW][hapmap];0.84[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.81[JPT][hapmap]
rs6539171	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs703681	0.85[CHD][hapmap]
rs7135015	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7138686	1.00[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.98[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7309240	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73193606	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7967503	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7968763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9668618	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs996294	0.87[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv899498	chr12:105173598-105461620	Flanking Active TSS Weak transcription Enhancers Strong 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	22 gene(s)	inside rSNPs	diseases
3	nsv832505	chr12:105315352-105497765	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2249454	C12orf23	cis	parietal	SCAN
rs2249454	CHST11	Cis_1M	lymphoblastoid	RTeQTL
rs2249454	C12orf42	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105290800-105331600	Weak transcription	Gastric	stomach
2	chr12:105304400-105324600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:105320200-105332200	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr12:105320600-105324600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:105321000-105324200	Weak transcription	HUVEC	blood vessel
6	chr12:105322400-105324800	Enhancers	NHDF-Ad	bronchial
7	chr12:105322800-105324200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr12:105323000-105325200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr12:105323200-105324600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr12:105323200-105324800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr12:105323200-105325200	Enhancers	HepG2	liver
12	chr12:105323200-105325800	Flanking Active TSS	GM12878-XiMat	blood
13	chr12:105323400-105324200	Enhancers	HSMM	muscle
14	chr12:105323400-105324400	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr12:105323400-105324800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr12:105323400-105325000	Enhancers	Aorta	Aorta
17	chr12:105323400-105325200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr12:105323400-105325600	Enhancers	Liver	Liver
19	chr12:105323600-105324400	Enhancers	HSMMtube	muscle
20	chr12:105323600-105325000	Enhancers	Primary hematopoietic stem cells	blood
21	chr12:105323600-105325000	Enhancers	Osteobl	bone
22	chr12:105323600-105325200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr12:105323600-105338000	Weak transcription	Pancreas	Pancrea
24	chr12:105323800-105324400	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr12:105323800-105325000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr12:105324000-105324200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr12:105324000-105324600	Enhancers	NH-A	brain
28	chr12:105324000-105324800	Enhancers	A549	lung
29	chr12:105324000-105325000	Enhancers	Muscle Satellite Cultured Cells	--

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