Variant report

Variant	rs12368199
Chromosome Location	chr12:121472167-121472168
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:121472155..121474661-chr12:121478426..121481122,2	K562	blood:
2	chr12:120729256..120731429-chr12:121471533..121473045,2	MCF-7	breast:
3	chr12:121471397..121473334-chr12:121474789..121478157,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135114	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000200795	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10849828	0.81[ASN][1000 genomes]
rs11065393	0.91[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.87[ASN][1000 genomes]
rs11065403	0.95[ASN][1000 genomes]
rs1169280	0.90[CHB][hapmap];0.92[ASN][1000 genomes]
rs1169304	0.81[ASN][1000 genomes]
rs1169307	0.87[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs12811390	0.89[CHB][hapmap];0.95[ASN][1000 genomes]
rs12819210	0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.92[ASN][1000 genomes]
rs1796419	0.89[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.88[ASN][1000 genomes]
rs2257813	0.87[ASN][1000 genomes]
rs2258227	0.90[CHB][hapmap];0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs2259697	0.92[ASN][1000 genomes]
rs2264779	0.87[ASN][1000 genomes]
rs2701180	0.89[ASN][1000 genomes]
rs2708105	0.81[ASN][1000 genomes]
rs2859394	0.89[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.90[ASN][1000 genomes]
rs2859402	0.81[ASN][1000 genomes]
rs3999413	0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs4556628	0.89[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	nsv832531	chr12:121440495-121604232	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv560454	chr12:121457073-121745742	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats 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	29 gene(s)	inside rSNPs	diseases
11	esv3421024	chr12:121471004-121493702	Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12368199	CABP1	cis	cerebellum	SCAN
rs12368199	SBNO1	cis	parietal	SCAN
rs12368199	HPD	cis	parietal	SCAN
rs12368199	C12orf43	cis	parietal	SCAN
rs12368199	FLJ12448	cis	multi-tissue	Pritchard

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121454400-121472200	Weak transcription	Primary T cells from cord blood	blood
2	chr12:121454400-121475800	Weak transcription	Adipose Nuclei	Adipose
3	chr12:121454400-121476000	Weak transcription	Rectal Smooth Muscle	rectum
4	chr12:121454400-121476400	Weak transcription	Right Atrium	heart
5	chr12:121454600-121476200	Weak transcription	Brain Hippocampus Middle	brain
6	chr12:121454600-121476200	Weak transcription	Gastric	stomach
7	chr12:121469400-121472200	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr12:121470200-121476200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr12:121470400-121476200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr12:121470600-121472200	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr12:121471000-121473000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr12:121471000-121474200	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr12:121471000-121476000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr12:121471200-121472200	Enhancers	Esophagus	oesophagus
15	chr12:121471200-121472400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr12:121471200-121472400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr12:121471200-121472400	Enhancers	Duodenum Mucosa	Duodenum
18	chr12:121471200-121472600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr12:121471200-121472600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr12:121471200-121473000	Enhancers	HMEC	breast
21	chr12:121471200-121473000	Enhancers	NHEK	skin
22	chr12:121471200-121473600	Enhancers	Lung	lung
23	chr12:121471200-121474200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
24	chr12:121471200-121475200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr12:121471200-121475400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr12:121471400-121472400	Flanking Active TSS	Hela-S3	cervix
27	chr12:121471400-121472800	Enhancers	Spleen	Spleen
28	chr12:121471400-121472800	Enhancers	A549	lung
29	chr12:121471400-121473000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr12:121471400-121473000	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr12:121471400-121473000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
32	chr12:121471400-121475200	Enhancers	HSMM	muscle
33	chr12:121471600-121472200	Enhancers	Monocytes-CD14+_RO01746	blood
34	chr12:121471600-121472400	Enhancers	GM12878-XiMat	blood
35	chr12:121471600-121472600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
36	chr12:121471600-121472600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr12:121471600-121472800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr12:121471600-121473000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
39	chr12:121471600-121473000	Enhancers	NHDF-Ad	bronchial
40	chr12:121471600-121473200	Enhancers	Fetal Thymus	thymus
41	chr12:121471600-121473200	Enhancers	Osteobl	bone
42	chr12:121471600-121474000	Weak transcription	Small Intestine	intestine
43	chr12:121471600-121476000	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr12:121471600-121476200	Weak transcription	Colonic Mucosa	Colon
45	chr12:121471800-121472200	Enhancers	Primary T cells fromperipheralblood	blood
46	chr12:121471800-121472200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr12:121471800-121472200	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr12:121471800-121472600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr12:121471800-121472600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
50	chr12:121471800-121472600	Enhancers	NH-A	brain

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