Variant report

Variant	rs6886199
Chromosome Location	chr5:112899250-112899251
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 102 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10038632	0.89[AMR][1000 genomes]
rs10039853	0.86[CHB][hapmap];0.89[AMR][1000 genomes]
rs10040203	0.86[CHB][hapmap]
rs10061552	0.86[CHB][hapmap];0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10063008	0.88[AMR][1000 genomes]
rs10071816	0.87[MEX][hapmap];0.89[AMR][1000 genomes]
rs10078214	0.86[YRI][hapmap]
rs10079603	0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs10079758	0.89[AMR][1000 genomes]
rs10079895	0.86[CHB][hapmap];0.89[AMR][1000 genomes]
rs10079973	0.86[CHB][hapmap];0.89[AMR][1000 genomes]
rs10080096	0.86[CHB][hapmap];0.84[AMR][1000 genomes]
rs1017209	0.87[CHD][hapmap];0.95[MEX][hapmap]
rs10477497	0.86[CHB][hapmap];0.89[AMR][1000 genomes]
rs10477498	0.85[AMR][1000 genomes]
rs10477499	0.86[CHB][hapmap]
rs10477500	0.86[CHB][hapmap]
rs10478127	0.85[CHB][hapmap];0.89[AMR][1000 genomes]
rs10478129	0.86[CHB][hapmap]
rs10478132	0.86[CHB][hapmap]
rs1052896	0.84[CHB][hapmap]
rs11241214	0.86[CHB][hapmap];0.91[CHD][hapmap];0.91[MEX][hapmap];0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11241215	0.83[CHB][hapmap]
rs11749931	0.86[CHB][hapmap];0.91[CHD][hapmap];0.91[MEX][hapmap];0.84[AMR][1000 genomes]
rs11956399	0.86[CHB][hapmap];0.89[AMR][1000 genomes]
rs12186798	0.86[CHB][hapmap];0.89[AMR][1000 genomes]
rs12519315	0.85[CEU][hapmap];0.86[ASN][1000 genomes]
rs12523145	0.88[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[ASN][1000 genomes]
rs12652172	0.80[AMR][1000 genomes]
rs12654189	0.84[AMR][1000 genomes]
rs12659978	0.81[JPT][hapmap]
rs12660001	0.85[CHB][hapmap];0.89[AMR][1000 genomes]
rs13359703	0.89[AMR][1000 genomes]
rs1820056	0.82[JPT][hapmap]
rs1833681	0.86[CHB][hapmap];0.91[CHD][hapmap];0.87[MEX][hapmap]
rs2162842	0.89[AMR][1000 genomes]
rs2288449	0.86[CHB][hapmap];0.91[CHD][hapmap];0.91[MEX][hapmap];0.88[AMR][1000 genomes]
rs26991	0.84[CEU][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs28558374	0.89[AMR][1000 genomes]
rs2910018	0.87[JPT][hapmap]
rs34514665	0.84[AMR][1000 genomes]
rs34864074	0.84[AMR][1000 genomes]
rs35162738	0.84[AMR][1000 genomes]
rs35526509	0.83[AMR][1000 genomes]
rs3763138	0.86[CHB][hapmap];0.91[CHD][hapmap];0.82[MEX][hapmap]
rs3763140	0.86[CHB][hapmap];0.89[AMR][1000 genomes]
rs3815911	0.91[CHD][hapmap];0.88[AMR][1000 genomes]
rs3936061	0.86[CHB][hapmap];0.91[CHD][hapmap];0.91[MEX][hapmap];0.84[AMR][1000 genomes]
rs4132094	0.81[AMR][1000 genomes]
rs4334877	0.86[CHB][hapmap];0.84[AMR][1000 genomes]
rs4415069	0.82[JPT][hapmap]
rs4588592	0.89[AMR][1000 genomes]
rs4639215	0.82[JPT][hapmap]
rs4705553	0.84[AMR][1000 genomes]
rs4705557	0.86[CHB][hapmap];0.88[AMR][1000 genomes]
rs4705825	0.87[CHD][hapmap];0.95[MEX][hapmap]
rs4705827	0.91[CHD][hapmap];0.87[MEX][hapmap]
rs4705828	1.00[CHB][hapmap]
rs4705830	0.81[JPT][hapmap]
rs56206672	0.88[AMR][1000 genomes]
rs58044020	0.89[AMR][1000 genomes]
rs60871281	0.89[AMR][1000 genomes]
rs60914066	0.89[AMR][1000 genomes]
rs6594721	0.87[CHD][hapmap];0.87[MEX][hapmap]
rs6594732	0.91[CHD][hapmap];0.87[MEX][hapmap]
rs6594733	0.91[CHD][hapmap];0.87[MEX][hapmap]
rs6594734	0.86[CHB][hapmap];0.91[CHD][hapmap];0.91[MEX][hapmap];0.89[AMR][1000 genomes]
rs6594735	1.00[ASW][hapmap];0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6867502	0.89[AMR][1000 genomes]
rs6877432	0.86[CHB][hapmap];0.90[CHD][hapmap];0.82[MEX][hapmap];0.89[AMR][1000 genomes]
rs6877466	0.89[AMR][1000 genomes]
rs6877834	0.89[AMR][1000 genomes]
rs6881976	0.81[JPT][hapmap]
rs6883383	0.86[CHB][hapmap];0.91[MEX][hapmap];0.88[AMR][1000 genomes]
rs6883547	0.80[LWK][hapmap];0.93[YRI][hapmap]
rs6883557	0.88[AMR][1000 genomes]
rs6886628	0.86[CHB][hapmap];0.91[CHD][hapmap];0.91[MEX][hapmap];0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6889501	0.89[AMR][1000 genomes]
rs6889574	0.86[CHB][hapmap];0.90[CHD][hapmap];0.91[MEX][hapmap];0.89[AMR][1000 genomes]
rs72805422	0.89[AMR][1000 genomes]
rs7349799	0.92[CHB][hapmap];0.89[AMR][1000 genomes]
rs7705562	0.86[CHB][hapmap]
rs7706215	0.89[AMR][1000 genomes]
rs7706958	0.86[CHB][hapmap];0.89[AMR][1000 genomes]
rs7711078	0.83[CHB][hapmap]
rs7711211	0.93[CHB][hapmap];0.90[CHD][hapmap];0.91[MEX][hapmap];0.89[AMR][1000 genomes]
rs7711367	0.86[CHB][hapmap];0.91[CHD][hapmap];0.91[MEX][hapmap];0.89[AMR][1000 genomes]
rs7713038	0.86[CHB][hapmap]
rs7713451	0.86[CHB][hapmap];0.90[CHD][hapmap];0.87[MEX][hapmap]
rs7722918	0.89[AMR][1000 genomes]
rs7729306	0.86[CHB][hapmap];0.91[CHD][hapmap];0.87[MEX][hapmap]
rs7730949	0.86[CHB][hapmap];0.91[CHD][hapmap]
rs7737023	0.86[CHB][hapmap];0.89[AMR][1000 genomes]
rs919304	0.86[CHB][hapmap];0.91[CHD][hapmap];0.91[MEX][hapmap];0.88[AMR][1000 genomes]
rs9326893	0.86[CHB][hapmap];0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9326895	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882720	chr5:112859994-112911165	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv882721	chr5:112859994-112963488	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
3	nsv882722	chr5:112868878-112899573	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv882723	chr5:112868878-112911165	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv882724	chr5:112868878-112933202	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv1033202	chr5:112891857-112945992	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6886199	DCP2	cis	parietal	SCAN
rs6886199	CDO1	cis	cerebellum	SCAN
rs6886199	YTHDC2	cis	parietal	SCAN
rs6886199	YTHDC2	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112850400-112904000	Weak transcription	Psoas Muscle	Psoas
2	chr5:112850600-112908400	Weak transcription	Colonic Mucosa	Colon
3	chr5:112851600-112902800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr5:112867000-112910000	Weak transcription	Right Ventricle	heart
5	chr5:112867200-112903400	Weak transcription	Pancreas	Pancrea
6	chr5:112867200-112904000	Weak transcription	Lung	lung
7	chr5:112867200-112904200	Weak transcription	Aorta	Aorta
8	chr5:112867200-112909800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr5:112867200-112909800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr5:112867200-112910000	Weak transcription	Esophagus	oesophagus
11	chr5:112867400-112926000	Weak transcription	Small Intestine	intestine
12	chr5:112867400-112933000	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr5:112868600-112911400	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr5:112869200-112910000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr5:112870200-112930800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr5:112872000-112904000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:112872000-112915000	Weak transcription	Hela-S3	cervix
18	chr5:112873000-112900600	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr5:112873400-112908800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr5:112874000-112909600	Weak transcription	Spleen	Spleen
21	chr5:112874400-112902600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:112876000-112918800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr5:112877200-112905800	Weak transcription	Fetal Stomach	stomach
24	chr5:112879600-112902800	Weak transcription	Thymus	Thymus
25	chr5:112879600-112904200	Weak transcription	Gastric	stomach
26	chr5:112881800-112906400	Weak transcription	Fetal Intestine Small	intestine
27	chr5:112882600-112904000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr5:112882800-112909600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr5:112883000-112899600	Weak transcription	Brain Angular Gyrus	brain
30	chr5:112883000-112903200	Weak transcription	Rectal Smooth Muscle	rectum
31	chr5:112883800-112907400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr5:112884200-112905200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr5:112884200-112905600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr5:112884200-112908000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr5:112886000-112902400	Weak transcription	NHLF	lung
36	chr5:112886600-112911200	Strong transcription	Primary B cells from peripheral blood	blood
37	chr5:112887800-112904400	Strong transcription	Fetal Intestine Large	intestine
38	chr5:112888000-112908200	Strong transcription	Liver	Liver
39	chr5:112888600-112901400	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr5:112888800-112908400	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr5:112889400-112930600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr5:112889600-112904000	Weak transcription	Fetal Heart	heart
43	chr5:112889800-112909600	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr5:112889800-112910000	Weak transcription	HSMMtube	muscle
45	chr5:112890400-112902400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr5:112890600-112915800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr5:112891600-112906600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr5:112891600-112908200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr5:112891600-112912600	Weak transcription	Stomach Mucosa	stomach
50	chr5:112891800-112903200	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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