Variant report

Variant	rs6869399
Chromosome Location	chr5:112440142-112440143
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10040400	0.89[ASN][1000 genomes]
rs10045658	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs10058407	0.81[CEU][hapmap]
rs10063834	0.81[EUR][1000 genomes]
rs10067901	1.00[CEU][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10074318	0.95[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10223151	0.86[CEU][hapmap]
rs10223152	0.86[CEU][hapmap]
rs10477486	0.81[CEU][hapmap]
rs10478102	0.81[CEU][hapmap]
rs10478110	0.89[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs11241190	0.81[CEU][hapmap]
rs11241191	0.90[ASN][1000 genomes]
rs11241192	0.90[ASN][1000 genomes]
rs11241193	0.90[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs11743369	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11744218	0.86[CEU][hapmap]
rs11744828	0.86[CEU][hapmap]
rs11744956	0.85[CEU][hapmap]
rs11746908	0.86[CEU][hapmap]
rs11750093	0.81[CEU][hapmap]
rs11953203	0.89[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs12188482	0.92[ASN][1000 genomes]
rs12517185	0.90[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs12517187	0.90[ASN][1000 genomes]
rs12523053	0.88[ASN][1000 genomes]
rs13156718	0.89[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13173830	0.91[CEU][hapmap];0.95[EUR][1000 genomes]
rs13174483	0.90[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs13179421	0.89[ASN][1000 genomes]
rs13183638	0.84[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs13184187	0.92[ASN][1000 genomes]
rs2227947	0.81[CEU][hapmap]
rs28645351	0.81[EUR][1000 genomes]
rs36041392	0.92[ASN][1000 genomes]
rs3884576	0.92[ASN][1000 genomes]
rs3890775	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs3890776	0.83[EUR][1000 genomes]
rs3922563	0.85[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs3922583	0.85[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs4078253	0.80[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs4078254	0.80[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs4235793	0.88[ASN][1000 genomes]
rs4262097	0.87[ASN][1000 genomes]
rs4283779	0.80[CEU][hapmap]
rs4397121	0.86[CEU][hapmap]
rs4463174	0.81[CEU][hapmap]
rs4645326	0.86[CEU][hapmap]
rs4705539	0.81[CEU][hapmap]
rs4705542	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[MKK][hapmap];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4705543	0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4705544	0.89[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs4705545	0.88[ASN][1000 genomes]
rs4705780	0.89[JPT][hapmap];0.81[MKK][hapmap];0.86[ASN][1000 genomes]
rs4705783	0.85[CHB][hapmap]
rs4705787	0.88[ASN][1000 genomes]
rs4705788	0.88[ASN][1000 genomes]
rs62374710	0.92[ASN][1000 genomes]
rs6594680	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs6594683	0.80[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs6859963	0.86[ASN][1000 genomes]
rs6861166	0.80[CEU][hapmap]
rs6862481	0.81[CEU][hapmap]
rs6866566	0.81[CEU][hapmap]
rs6866706	0.81[CEU][hapmap]
rs6873623	0.86[CEU][hapmap]
rs6874220	0.81[EUR][1000 genomes]
rs6874314	0.81[EUR][1000 genomes]
rs6874595	0.81[EUR][1000 genomes]
rs6879138	0.86[CEU][hapmap]
rs6879633	0.81[CEU][hapmap]
rs6879942	0.86[CEU][hapmap]
rs6898297	0.81[CEU][hapmap]
rs7700271	0.90[ASN][1000 genomes]
rs7704382	0.90[ASN][1000 genomes]
rs7707142	0.87[ASN][1000 genomes]
rs7708475	0.81[EUR][1000 genomes]
rs7713290	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs7713336	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs7714010	0.86[CEU][hapmap]
rs7714160	0.86[CEU][hapmap]
rs7714492	0.86[CEU][hapmap]
rs7714725	0.82[CEU][hapmap]
rs7731180	0.91[ASN][1000 genomes]
rs7734411	0.83[CEU][hapmap]
rs7736823	0.86[CEU][hapmap]
rs9326874	0.86[CEU][hapmap]
rs9326875	0.86[CEU][hapmap]
rs9326877	0.90[ASN][1000 genomes]
rs9326878	0.90[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs9326879	0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs9885385	0.90[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	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	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
3	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6869399	YTHDC2	cis	cerebellum	SCAN

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112384000-112453000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr5:112399800-112441800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr5:112411200-112443400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr5:112418400-112441600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr5:112418600-112441400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:112424400-112448000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr5:112426000-112441600	Weak transcription	Colon Smooth Muscle	Colon
8	chr5:112426200-112445000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr5:112426600-112453000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr5:112426800-112450200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr5:112426800-112450600	Weak transcription	Primary T cells from cord blood	blood
12	chr5:112426800-112450600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr5:112426800-112453800	Weak transcription	HSMMtube	muscle
14	chr5:112427000-112440800	Weak transcription	NH-A	brain
15	chr5:112427000-112453800	Weak transcription	Fetal Kidney	kidney
16	chr5:112427200-112448200	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr5:112427600-112441600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr5:112427600-112442000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr5:112427600-112443200	Weak transcription	Brain Substantia Nigra	brain
20	chr5:112428000-112440200	Strong transcription	Liver	Liver
21	chr5:112428400-112440200	Strong transcription	Fetal Stomach	stomach
22	chr5:112428600-112445000	Weak transcription	Placenta	Placenta
23	chr5:112430400-112441000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr5:112431000-112442600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr5:112431200-112461600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr5:112431600-112440200	Strong transcription	Ovary	ovary
27	chr5:112432200-112443200	Weak transcription	Lung	lung
28	chr5:112432200-112450200	Weak transcription	Spleen	Spleen
29	chr5:112432200-112454600	Weak transcription	Pancreas	Pancrea
30	chr5:112433600-112441200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr5:112433800-112443800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr5:112434000-112459200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr5:112436000-112442400	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr5:112436400-112440600	Strong transcription	Stomach Smooth Muscle	stomach
35	chr5:112436800-112441400	Strong transcription	NHEK	skin
36	chr5:112437000-112440200	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr5:112437600-112445800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr5:112437800-112454400	Weak transcription	Fetal Muscle Trunk	muscle
39	chr5:112438000-112440200	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr5:112438000-112444400	Weak transcription	HMEC	breast
41	chr5:112438000-112450600	Weak transcription	Aorta	Aorta
42	chr5:112438000-112454200	Weak transcription	Psoas Muscle	Psoas
43	chr5:112438200-112444800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr5:112438200-112450000	Weak transcription	Adipose Nuclei	Adipose
45	chr5:112438200-112450200	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr5:112438200-112452800	Weak transcription	Brain Anterior Caudate	brain
47	chr5:112438400-112443000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr5:112438400-112443000	Weak transcription	Brain Cingulate Gyrus	brain
49	chr5:112438800-112440200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr5:112438800-112440400	Enhancers	Fetal Heart	heart

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