Variant report

Variant	rs17135753
Chromosome Location	chr5:112928779-112928780
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 96 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10039853	0.94[CEU][hapmap]
rs10053582	0.81[CEU][hapmap]
rs10061552	0.94[CEU][hapmap]
rs10063008	0.80[EUR][1000 genomes]
rs10071816	0.94[CEU][hapmap]
rs10079895	0.94[CEU][hapmap]
rs10079973	0.94[CEU][hapmap]
rs10080096	0.89[CEU][hapmap]
rs10477497	0.88[CEU][hapmap]
rs10478127	0.94[CEU][hapmap]
rs11241206	1.00[JPT][hapmap];0.85[MEX][hapmap]
rs11241214	0.94[CEU][hapmap]
rs11241215	0.88[CEU][hapmap]
rs11747924	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.87[YRI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11748145	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11748794	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11749931	0.94[CEU][hapmap]
rs11956399	0.94[CEU][hapmap]
rs12186798	0.94[CEU][hapmap]
rs12517582	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs12519323	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12660001	0.94[CEU][hapmap]
rs13359703	0.80[EUR][1000 genomes]
rs17135608	1.00[JPT][hapmap]
rs17135616	1.00[JPT][hapmap]
rs17135630	0.86[JPT][hapmap]
rs17135754	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1833678	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2042222	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2195380	0.88[ASN][1000 genomes]
rs2288449	0.94[CEU][hapmap]
rs2416281	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28842543	0.83[ASN][1000 genomes]
rs3763140	0.94[CEU][hapmap]
rs3815911	0.94[CEU][hapmap]
rs3846721	1.00[JPT][hapmap];0.85[MEX][hapmap]
rs3846722	1.00[CEU][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3936061	0.94[CEU][hapmap]
rs4122546	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4334877	0.88[CEU][hapmap]
rs4588592	0.94[CEU][hapmap]
rs4705551	1.00[CEU][hapmap];0.88[JPT][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4705557	0.94[CEU][hapmap]
rs4705558	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4705819	1.00[JPT][hapmap]
rs4705826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57077871	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6594734	0.94[CEU][hapmap]
rs6594737	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs66490974	0.85[EUR][1000 genomes]
rs66497221	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs67020702	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67103739	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs67723806	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6859688	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6861786	0.80[EUR][1000 genomes]
rs6864369	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6864528	1.00[JPT][hapmap];0.85[MEX][hapmap]
rs6877432	0.89[CEU][hapmap]
rs6878001	1.00[CEU][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.88[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6879800	0.87[CHD][hapmap];0.88[JPT][hapmap];0.90[MEX][hapmap]
rs6882900	0.81[EUR][1000 genomes]
rs6883383	0.94[CEU][hapmap];0.80[TSI][hapmap]
rs6883441	1.00[CEU][hapmap];0.88[JPT][hapmap];0.85[EUR][1000 genomes]
rs6884704	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6886628	0.94[CEU][hapmap]
rs6889574	0.94[CEU][hapmap]
rs6896469	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6896501	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6898425	0.81[CEU][hapmap]
rs72794121	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72805465	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73241779	0.85[EUR][1000 genomes]
rs73242809	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73247445	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7349799	0.87[CEU][hapmap]
rs7702833	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7705562	0.94[CEU][hapmap]
rs7706958	0.94[CEU][hapmap]
rs7707443	1.00[CEU][hapmap];0.88[JPT][hapmap];0.84[EUR][1000 genomes]
rs7711078	0.87[CEU][hapmap]
rs7711211	0.94[CEU][hapmap]
rs7711367	0.94[CEU][hapmap]
rs7729433	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7737023	0.94[CEU][hapmap]
rs919304	0.94[CEU][hapmap]
rs9326893	0.94[CEU][hapmap]
rs957777	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	nsv520674	chr5:112911165-112942820	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
5	esv2752057	chr5:112916398-112945992	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv1029507	chr5:112916398-112945992	Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
7	esv2763910	chr5:112916398-112951827	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
8	nsv1031336	chr5:112916398-112956588	Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	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
rs17135753	YTHDC2	cis	parietal	SCAN
rs17135753	DCP2	cis	parietal	SCAN
rs17135753	YTHDC2	cis	cerebellum	SCAN
rs17135753	YTHDC2	cis	multi-tissue	Pritchard

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112867400-112933000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr5:112870200-112930800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr5:112889400-112930600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr5:112899400-112929400	Weak transcription	HepG2	liver
5	chr5:112904600-112934800	Weak transcription	Psoas Muscle	Psoas
6	chr5:112907400-112932000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr5:112908800-112935200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr5:112910600-112933400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr5:112910600-112935200	Weak transcription	Spleen	Spleen
10	chr5:112910600-112935400	Weak transcription	Colon Smooth Muscle	Colon
11	chr5:112910600-112936600	Weak transcription	Colonic Mucosa	Colon
12	chr5:112910600-112942000	Weak transcription	Brain Substantia Nigra	brain
13	chr5:112910800-112929200	Weak transcription	Right Ventricle	heart
14	chr5:112910800-112929400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr5:112910800-112930400	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr5:112910800-112933600	Weak transcription	Brain Cingulate Gyrus	brain
17	chr5:112910800-112933600	Weak transcription	Fetal Stomach	stomach
18	chr5:112910800-112934600	Weak transcription	Gastric	stomach
19	chr5:112910800-112935000	Weak transcription	Pancreas	Pancrea
20	chr5:112910800-112935200	Weak transcription	Esophagus	oesophagus
21	chr5:112910800-112937400	Weak transcription	Fetal Intestine Small	intestine
22	chr5:112910800-112938200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr5:112910800-112942200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr5:112911000-112930000	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr5:112911200-112929000	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr5:112916000-112931400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr5:112916400-112929200	Weak transcription	Lung	lung
28	chr5:112916400-112930400	Weak transcription	NHLF	lung
29	chr5:112916400-112933000	Weak transcription	Thymus	Thymus
30	chr5:112916400-112933400	Weak transcription	Aorta	Aorta
31	chr5:112916800-112936000	Weak transcription	Fetal Heart	heart
32	chr5:112917200-112942000	Weak transcription	K562	blood
33	chr5:112917400-112928800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr5:112917400-112929600	Weak transcription	Fetal Brain Male	brain
35	chr5:112917400-112937600	Weak transcription	HSMMtube	muscle
36	chr5:112917800-112933400	Weak transcription	Brain Angular Gyrus	brain
37	chr5:112918000-112933600	Weak transcription	Hela-S3	cervix
38	chr5:112918000-112939000	Weak transcription	NHEK	skin
39	chr5:112920400-112939000	Weak transcription	HMEC	breast
40	chr5:112920600-112934600	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr5:112920600-112934800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr5:112920600-112936000	Weak transcription	Brain Anterior Caudate	brain
43	chr5:112920800-112928800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr5:112920800-112930200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr5:112920800-112934000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr5:112920800-112938600	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr5:112920800-112942000	Weak transcription	Ovary	ovary
48	chr5:112922000-112929000	Weak transcription	Fetal Brain Female	brain
49	chr5:112922000-112933400	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr5:112923600-112933600	Strong transcription	Monocytes-CD14+_RO01746	blood

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