Variant report

Variant	rs10478102
Chromosome Location	chr5:112398770-112398771
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112398620..112400244-chr5:112402557..112404477,2	K562	blood:

Extended variants
information (count: 91 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10045658	0.95[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10053994	0.85[EUR][1000 genomes]
rs10058407	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10063834	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10078431	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10223151	0.95[CEU][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10223152	0.95[CEU][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10477486	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10478106	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11241190	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11744218	0.95[CEU][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11744828	0.95[CEU][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11744956	0.95[CEU][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11746908	0.95[CEU][hapmap];0.82[GIH][hapmap]
rs11750093	1.00[CEU][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11960706	1.00[JPT][hapmap]
rs12513669	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13173830	0.91[CEU][hapmap]
rs13174818	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2227947	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2227950	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28645351	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28774401	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs36182962	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3890775	0.95[CEU][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3890776	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4235788	0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4283779	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4397121	0.95[CEU][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4463174	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4645326	0.95[CEU][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4705539	1.00[CEU][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56054154	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6594665	0.81[CHB][hapmap]
rs6594672	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6594673	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6594675	0.94[EUR][1000 genomes]
rs6594679	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6594680	0.95[CEU][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6859813	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6861166	1.00[CEU][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6862481	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6863319	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6865444	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6866442	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6866566	1.00[CEU][hapmap];0.83[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6866706	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6866718	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6869383	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6869399	0.81[CEU][hapmap]
rs6873623	0.95[CEU][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs6874220	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6874314	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6874595	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6874727	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6878846	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6879138	0.95[CEU][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6879633	1.00[CEU][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6879634	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6879942	0.95[CEU][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6882689	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6894700	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6898297	1.00[CEU][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7708475	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7713290	0.95[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7713336	0.95[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7714010	0.95[CEU][hapmap];0.82[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7714160	0.95[CEU][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7714275	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7714334	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7714349	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7714363	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7714492	0.95[CEU][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7714725	0.91[CEU][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7724258	0.93[GIH][hapmap]
rs7728858	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7728921	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7730767	0.81[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7732048	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7734411	0.94[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7734511	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7736823	0.95[CEU][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7737329	0.91[EUR][1000 genomes]
rs9326874	0.95[CEU][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9326875	0.95[CEU][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]

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	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv882717	chr5:112336588-112408944	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
3	esv15902	chr5:112369563-112410775	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv599395	chr5:112370311-112428869	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1018344	chr5:112390951-112458853	Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1032798	chr5:112392380-112408177	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10478102	YTHDC2	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112363800-112399000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr5:112363800-112409200	Weak transcription	Colonic Mucosa	Colon
3	chr5:112363800-112417800	Weak transcription	Duodenum Mucosa	Duodenum
4	chr5:112370200-112406600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:112371400-112423800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr5:112373000-112398800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr5:112373200-112399000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr5:112375000-112402600	Weak transcription	Pancreas	Pancrea
9	chr5:112379600-112399600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr5:112379600-112424200	Weak transcription	Psoas Muscle	Psoas
11	chr5:112383200-112409400	Strong transcription	Liver	Liver
12	chr5:112384000-112453000	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr5:112384200-112411000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr5:112384600-112398800	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr5:112384800-112399000	Weak transcription	Aorta	Aorta
16	chr5:112388400-112398800	Weak transcription	Colon Smooth Muscle	Colon
17	chr5:112388800-112402400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr5:112390600-112402400	Weak transcription	Spleen	Spleen
19	chr5:112390800-112410800	Weak transcription	Fetal Intestine Small	intestine
20	chr5:112391600-112439000	Weak transcription	Gastric	stomach
21	chr5:112392800-112399000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr5:112393600-112400200	Weak transcription	Placenta	Placenta
23	chr5:112394000-112399200	Weak transcription	Ovary	ovary
24	chr5:112394000-112399400	Enhancers	Fetal Thymus	thymus
25	chr5:112394600-112399000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr5:112394800-112400800	Strong transcription	Esophagus	oesophagus
27	chr5:112395000-112411600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr5:112395400-112399000	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr5:112395600-112399000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr5:112395600-112399400	Weak transcription	Right Atrium	heart
31	chr5:112395600-112399600	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr5:112395600-112399600	Enhancers	NHDF-Ad	bronchial
33	chr5:112395600-112400000	Enhancers	Brain Germinal Matrix	brain
34	chr5:112395600-112401400	Weak transcription	Lung	lung
35	chr5:112395600-112402400	Weak transcription	Rectal Smooth Muscle	rectum
36	chr5:112395600-112403400	Weak transcription	Brain Cingulate Gyrus	brain
37	chr5:112395600-112403600	Weak transcription	Fetal Brain Male	brain
38	chr5:112395600-112417600	Weak transcription	Brain Angular Gyrus	brain
39	chr5:112395600-112420400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr5:112395800-112399000	Weak transcription	HUVEC	blood vessel
41	chr5:112395800-112402600	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr5:112395800-112408600	Weak transcription	Brain Anterior Caudate	brain
43	chr5:112395800-112409000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr5:112396000-112417200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr5:112396200-112402600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr5:112396400-112398800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr5:112396600-112399000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr5:112396600-112400600	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr5:112396800-112399000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr5:112396800-112399200	Enhancers	HSMM	muscle

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