Variant report

Variant	rs12367872
Chromosome Location	chr12:50607834-50607835
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10506292	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap]
rs10783344	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.92[YRI][hapmap]
rs10876014	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap]
rs10876015	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs10876017	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap]
rs10876023	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap]
rs10876024	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap]
rs11169315	1.00[CEU][hapmap]
rs11169322	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap]
rs11169331	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11169332	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs11169335	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs11169348	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs11169350	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap]
rs11169351	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs11169357	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.91[YRI][hapmap]
rs11169360	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.92[YRI][hapmap]
rs11169370	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap]
rs11833608	1.00[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.88[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap]
rs11838347	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap]
rs12303082	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs12422417	1.00[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs12424691	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap]
rs12424713	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap]
rs12425705	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs12828340	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap]
rs1362983	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap]
rs2111988	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap]
rs2302900	0.96[CEU][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap]
rs2358539	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs3812825	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.88[LWK][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap]
rs4348979	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.98[TSI][hapmap]
rs4421818	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap]
rs4768951	0.96[CEU][hapmap]
rs6580736	0.96[CEU][hapmap];0.89[TSI][hapmap]
rs6580738	0.96[CEU][hapmap];0.89[TSI][hapmap]
rs7132551	1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs7134595	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.88[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap]
rs7138420	0.96[CEU][hapmap];0.80[TSI][hapmap]
rs7138622	0.96[CEU][hapmap]
rs7296291	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs7311973	1.00[CEU][hapmap]
rs7312252	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap]
rs7315690	0.96[CEU][hapmap];0.80[TSI][hapmap]
rs7486747	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.90[LWK][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap]
rs7953953	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap]
rs7979830	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];0.91[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv899075	chr12:50594947-50835060	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
4	nsv976744	chr12:50604432-50610917	Weak transcription Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12367872	LASS5	cis	cerebellum	SCAN
rs12367872	LASS5	cis	parietal	SCAN
rs12367872	DIP2B	Cis_1M	lymphoblastoid	RTeQTL
rs12367872	SLC38A1	cis	parietal	SCAN
rs12367872	CELA1	cis	parietal	SCAN
rs12367872	FAIM2	cis	cerebellum	SCAN

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50571800-50614200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:50572200-50614000	Weak transcription	Right Ventricle	heart
3	chr12:50582800-50614000	Weak transcription	Brain Angular Gyrus	brain
4	chr12:50582800-50614200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr12:50583000-50614400	Weak transcription	Brain Anterior Caudate	brain
6	chr12:50591600-50615600	Weak transcription	HepG2	liver
7	chr12:50593400-50614200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr12:50593400-50614200	Weak transcription	Fetal Brain Male	brain
9	chr12:50593400-50614600	Weak transcription	Esophagus	oesophagus
10	chr12:50596200-50613400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr12:50596800-50614000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr12:50597800-50608800	Strong transcription	Fetal Intestine Large	intestine
13	chr12:50598400-50611400	Weak transcription	Spleen	Spleen
14	chr12:50598400-50613400	Weak transcription	K562	blood
15	chr12:50598600-50612400	Weak transcription	Psoas Muscle	Psoas
16	chr12:50598600-50613400	Weak transcription	Aorta	Aorta
17	chr12:50598600-50613400	Weak transcription	Fetal Kidney	kidney
18	chr12:50598600-50614000	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr12:50598600-50614000	Weak transcription	Brain Germinal Matrix	brain
20	chr12:50599000-50612000	Weak transcription	Gastric	stomach
21	chr12:50599000-50614200	Weak transcription	Fetal Brain Female	brain
22	chr12:50599200-50614200	Weak transcription	Brain Cingulate Gyrus	brain
23	chr12:50599400-50614000	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr12:50599400-50615000	Weak transcription	Liver	Liver
25	chr12:50599600-50610200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr12:50599600-50613400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr12:50599600-50613400	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr12:50599600-50614000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr12:50599600-50614000	Weak transcription	Brain Hippocampus Middle	brain
30	chr12:50599600-50614000	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr12:50599800-50608400	Weak transcription	Small Intestine	intestine
32	chr12:50599800-50608800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr12:50599800-50612400	Weak transcription	Colon Smooth Muscle	Colon
34	chr12:50599800-50613400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr12:50599800-50613600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr12:50599800-50614000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr12:50599800-50614000	Weak transcription	Left Ventricle	heart
38	chr12:50599800-50614600	Weak transcription	Ovary	ovary
39	chr12:50599800-50635800	Weak transcription	Pancreas	Pancrea
40	chr12:50600000-50613400	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr12:50600000-50613600	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr12:50600000-50615800	Weak transcription	Lung	lung
43	chr12:50600200-50611200	Weak transcription	Stomach Smooth Muscle	stomach
44	chr12:50600200-50613400	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr12:50600200-50614000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr12:50600200-50614200	Weak transcription	Primary hematopoietic stem cells	blood
47	chr12:50600600-50609600	Weak transcription	Fetal Lung	lung
48	chr12:50600600-50614000	Weak transcription	Colonic Mucosa	Colon
49	chr12:50603000-50611000	Weak transcription	Fetal Muscle Trunk	muscle
50	chr12:50603200-50611400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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