Variant report

Variant	rs2259816
Chromosome Location	chr12:121435587-121435588
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1169286	0.84[CHD][hapmap];0.90[JPT][hapmap]
rs1169300	0.95[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1169301	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1169303	0.83[MEX][hapmap]
rs1169306	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1169309	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1169310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1169311	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1169312	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1169313	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1169314	0.95[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1169315	0.92[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1182933	0.86[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.94[ASN][1000 genomes]
rs1183910	0.91[YRI][hapmap]
rs2254971	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2257764	0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2257962	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2258043	0.83[MEX][hapmap]
rs2258287	0.86[MEX][hapmap]
rs2259820	0.95[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs2259852	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2264750	0.97[ASN][1000 genomes]
rs2264782	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2393791	0.83[GIH][hapmap]
rs2464195	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2464196	0.95[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[YRI][hapmap];0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3213545	0.82[CHB][hapmap];0.82[YRI][hapmap]
rs4278584	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7310409	0.83[GIH][hapmap]
rs735396	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv899559	chr12:121324727-121592689	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv899560	chr12:121371233-121560581	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv899561	chr12:121376416-121525591	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv899562	chr12:121376416-121565870	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv1037195	chr12:121408540-121470375	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	esv2758318	chr12:121415845-121584813	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
9	esv2759917	chr12:121415845-121584813	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
10	nsv1039216	chr12:121421701-121538491	Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

Variant related diseases (count:2)

Disease	PMID	Source
C-reactive protein	22939635	GWAS catalog
Coronary heart disease	19198612	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2259816	FLJ12448	cis	multi-tissue	Pritchard
rs2259816	CABP1	cis	cerebellum	SCAN
rs2259816	C12orf43	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121418600-121441000	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr12:121418800-121439400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr12:121419600-121441000	Weak transcription	Small Intestine	intestine
4	chr12:121426200-121440200	Strong transcription	HepG2	liver
5	chr12:121427600-121442600	Strong transcription	Fetal Intestine Large	intestine
6	chr12:121427800-121441200	Strong transcription	Fetal Intestine Small	intestine
7	chr12:121429800-121442000	Strong transcription	Duodenum Mucosa	Duodenum
8	chr12:121429800-121451600	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr12:121431200-121435800	Strong transcription	Gastric	stomach
10	chr12:121431200-121439200	Strong transcription	Rectal Mucosa Donor 31	rectum
11	chr12:121431200-121440600	Weak transcription	Fetal Lung	lung
12	chr12:121431400-121435800	Strong transcription	Pancreas	Pancrea
13	chr12:121431600-121435600	Strong transcription	Colonic Mucosa	Colon
14	chr12:121432600-121441200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:121433200-121436600	Weak transcription	Stomach Mucosa	stomach
16	chr12:121433200-121448200	Weak transcription	Fetal Kidney	kidney
17	chr12:121433400-121435800	Strong transcription	Fetal Stomach	stomach
18	chr12:121433400-121437800	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr12:121433600-121440600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr12:121433800-121437000	Weak transcription	Right Atrium	heart
21	chr12:121434600-121437600	Weak transcription	A549	lung
22	chr12:121435000-121438000	Genic enhancers	Liver	Liver
23	chr12:121435200-121435800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr12:121435400-121435600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr12:121435400-121435600	Enhancers	Fetal Thymus	thymus
26	chr12:121435400-121435600	Bivalent Enhancer	Stomach Smooth Muscle	stomach
27	chr12:121435400-121435800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr12:121435400-121437400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr12:121435400-121438400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr12:121435400-121438800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:121435400-121441200	Weak transcription	HSMM	muscle

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