Variant report

Variant	rs11181461
Chromosome Location	chr12:42758931-42758932
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:42719576..42721367-chr12:42758087..42760933,2	MCF-7	breast:
2	chr12:42757559..42759561-chr12:42762947..42765091,2	MCF-7	breast:
3	chr12:42744561..42747064-chr12:42757512..42759146,2	K562	blood:

Variant related genes	Relation type
ENSG00000139168	Chromatin interaction
ENSG00000134283	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1043652	0.95[MEX][hapmap]
rs1043656	0.87[JPT][hapmap];0.87[MEX][hapmap]
rs1069644	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs10880275	0.91[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.80[JPT][hapmap];0.87[MEX][hapmap]
rs10880279	0.91[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.80[JPT][hapmap];0.87[MEX][hapmap]
rs10880282	0.94[ASN][1000 genomes]
rs10880284	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11181421	0.97[ASN][1000 genomes]
rs11181453	0.99[ASN][1000 genomes]
rs11181484	0.97[ASN][1000 genomes]
rs12229224	0.92[ASN][1000 genomes]
rs12229266	0.87[JPT][hapmap]
rs12231335	0.87[JPT][hapmap]
rs1238290	0.91[CHB][hapmap];0.89[CHD][hapmap];0.80[JPT][hapmap]
rs12423383	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1376931	0.86[MEX][hapmap]
rs1629725	0.97[ASN][1000 genomes]
rs1669888	0.90[ASN][1000 genomes]
rs1669891	0.94[ASN][1000 genomes]
rs1669901	0.97[ASN][1000 genomes]
rs1669903	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1669911	0.97[ASN][1000 genomes]
rs1669914	0.97[ASN][1000 genomes]
rs17091052	0.88[ASN][1000 genomes]
rs1796354	0.92[ASN][1000 genomes]
rs1796357	0.91[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[ASN][1000 genomes]
rs1796379	0.97[ASN][1000 genomes]
rs1796387	0.97[ASN][1000 genomes]
rs1796389	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1796392	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1796396	0.94[ASN][1000 genomes]
rs1796397	0.93[ASN][1000 genomes]
rs1796398	1.00[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.94[ASN][1000 genomes]
rs2243465	0.91[MEX][hapmap]
rs2406969	0.94[ASN][1000 genomes]
rs2600912	0.96[ASN][1000 genomes]
rs2708069	0.96[ASN][1000 genomes]
rs2708075	0.96[ASN][1000 genomes]
rs2708506	0.97[ASN][1000 genomes]
rs3213989	0.87[JPT][hapmap];0.91[MEX][hapmap]
rs3761677	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3827524	1.00[CHB][hapmap];0.93[JPT][hapmap];0.99[ASN][1000 genomes]
rs4603368	0.99[ASN][1000 genomes]
rs4768397	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.93[JPT][hapmap];0.81[MEX][hapmap];0.97[ASN][1000 genomes]
rs4768398	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4768401	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.99[ASN][1000 genomes]
rs4768412	0.82[JPT][hapmap];0.91[MEX][hapmap]
rs6582392	0.91[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.80[JPT][hapmap];0.87[MEX][hapmap]
rs712119	0.91[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.80[JPT][hapmap]
rs712120	0.84[CEU][hapmap];0.91[CHB][hapmap];0.80[JPT][hapmap];0.87[AFR][1000 genomes]
rs712122	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs712123	0.91[CHB][hapmap];0.89[CHD][hapmap];0.80[JPT][hapmap]
rs712125	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs712129	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs7134895	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs73122408	0.99[ASN][1000 genomes]
rs73122418	0.99[ASN][1000 genomes]
rs752767	0.99[ASN][1000 genomes]
rs7956016	0.91[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.80[JPT][hapmap]
rs7960176	0.91[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.80[JPT][hapmap];0.87[MEX][hapmap]
rs7970115	0.91[CHB][hapmap]
rs824741	0.91[CHB][hapmap];0.80[JPT][hapmap]
rs896555	0.91[MEX][hapmap]
rs896556	0.94[ASN][1000 genomes]

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	nsv1048971	chr12:42651976-42801204	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1044790	chr12:42672255-43344184	Enhancers Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
3	nsv541483	chr12:42672255-43344184	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11181461	PLCD3	trans	cerebellum	SCAN
rs11181461	CPNE8	cis	parietal	SCAN
rs11181461	KIF21A	cis	parietal	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:42720800-42844400	Weak transcription	Small Intestine	intestine
2	chr12:42721600-42769000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:42721600-42778600	Weak transcription	Spleen	Spleen
4	chr12:42721600-42800800	Weak transcription	Psoas Muscle	Psoas
5	chr12:42721600-42803600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr12:42721800-42769600	Weak transcription	Brain Substantia Nigra	brain
7	chr12:42721800-42769800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr12:42721800-42797000	Weak transcription	NHLF	lung
9	chr12:42721800-42803600	Weak transcription	Gastric	stomach
10	chr12:42722000-42769600	Weak transcription	Brain Anterior Caudate	brain
11	chr12:42722000-42769600	Weak transcription	Stomach Smooth Muscle	stomach
12	chr12:42722000-42772600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr12:42722000-42793200	Weak transcription	Fetal Kidney	kidney
14	chr12:42722200-42769200	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr12:42730800-42769600	Weak transcription	NH-A	brain
16	chr12:42731000-42768800	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr12:42731400-42769600	Weak transcription	Fetal Lung	lung
18	chr12:42731800-42770400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr12:42732200-42781200	Weak transcription	Fetal Brain Female	brain
20	chr12:42732200-42794400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr12:42732400-42763600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr12:42732400-42769600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr12:42733400-42796800	Weak transcription	Brain Hippocampus Middle	brain
24	chr12:42738000-42787400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr12:42738200-42823200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr12:42746000-42778400	Weak transcription	Fetal Brain Male	brain
27	chr12:42746600-42769800	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr12:42747400-42768800	Weak transcription	NHDF-Ad	bronchial
29	chr12:42747600-42769000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr12:42748200-42763600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr12:42750200-42762000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr12:42750400-42763000	Weak transcription	Colon Smooth Muscle	Colon
33	chr12:42750400-42768600	Weak transcription	Fetal Intestine Large	intestine
34	chr12:42750400-42768600	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr12:42750400-42768800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr12:42750400-42769000	Weak transcription	Ovary	ovary
37	chr12:42750400-42769000	Weak transcription	Osteobl	bone
38	chr12:42750400-42769200	Weak transcription	Left Ventricle	heart
39	chr12:42750400-42769400	Weak transcription	Fetal Muscle Trunk	muscle
40	chr12:42750400-42769600	Weak transcription	HSMMtube	muscle
41	chr12:42750400-42770200	Weak transcription	Fetal Muscle Leg	muscle
42	chr12:42750400-42770200	Weak transcription	Fetal Stomach	stomach
43	chr12:42750400-42770200	Weak transcription	Thymus	Thymus
44	chr12:42750600-42760600	Weak transcription	Fetal Heart	heart
45	chr12:42750600-42766000	Weak transcription	Aorta	Aorta
46	chr12:42750600-42769400	Weak transcription	Placenta	Placenta
47	chr12:42750800-42769200	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr12:42750800-42769800	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr12:42751200-42763200	Weak transcription	Primary B cells from cord blood	blood
50	chr12:42751200-42763600	Weak transcription	H1 Cell Line	embryonic stem cell

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