Variant report

Variant	rs4108702
Chromosome Location	chr5:112627269-112627270
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112608585..112610553-chr5:112626855..112628809,2	MCF-7	breast:
2	chr5:112616654..112618757-chr5:112626610..112628435,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10055089	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10056847	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10067046	0.81[CHD][hapmap];0.96[MEX][hapmap]
rs10068622	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10076501	0.92[MEX][hapmap]
rs10900683	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10900684	0.92[MEX][hapmap]
rs11241198	0.93[ASW][hapmap];0.95[CEU][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11241200	0.87[MEX][hapmap]
rs11741333	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11744824	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11956139	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13153071	0.91[MEX][hapmap]
rs13182478	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13182700	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1838204	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1838205	0.90[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.97[ASN][1000 genomes]
rs1873927	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34512273	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4108701	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4705812	0.92[MEX][hapmap]
rs485210	0.84[MEX][hapmap]
rs492346	0.84[MEX][hapmap]
rs6594699	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6594700	0.81[CHD][hapmap];0.92[MEX][hapmap]
rs7722276	0.84[MEX][hapmap]
rs7729163	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs971372	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][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	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
2	nsv882718	chr5:112519471-112674376	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv882719	chr5:112568212-112706511	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1024747	chr5:112592710-112679373	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1018078	chr5:112615220-112657404	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv949165	chr5:112615626-112730216	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4108702	YTHDC2	cis	cerebellum	SCAN
rs4108702	YTHDC2	cis	parietal	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112608000-112628200	Weak transcription	HMEC	breast
2	chr5:112610000-112628200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr5:112611000-112628200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr5:112617800-112628600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr5:112618400-112628000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr5:112618400-112628200	Weak transcription	Fetal Kidney	kidney
7	chr5:112618400-112628200	Weak transcription	Stomach Smooth Muscle	stomach
8	chr5:112618400-112628400	Weak transcription	Fetal Stomach	stomach
9	chr5:112619000-112628600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr5:112619000-112628800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr5:112620000-112628200	Weak transcription	Brain Anterior Caudate	brain
12	chr5:112620000-112628200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr5:112624000-112628000	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr5:112624000-112628600	Weak transcription	Esophagus	oesophagus
15	chr5:112624000-112628800	Weak transcription	Gastric	stomach
16	chr5:112625200-112628200	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr5:112625400-112627800	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr5:112625400-112628800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr5:112626000-112628200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr5:112626400-112628000	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr5:112626400-112628200	Enhancers	HUVEC	blood vessel
22	chr5:112626600-112627400	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr5:112626800-112627400	Enhancers	Right Atrium	heart
24	chr5:112626800-112627400	Enhancers	Right Ventricle	heart
25	chr5:112626800-112627600	Enhancers	H1 Cell Line	embryonic stem cell
26	chr5:112626800-112627600	Enhancers	H9 Cell Line	embryonic stem cell
27	chr5:112626800-112627600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr5:112626800-112627600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr5:112626800-112628400	Enhancers	Liver	Liver
30	chr5:112626800-112628600	Enhancers	Fetal Heart	heart
31	chr5:112626800-112631400	Active TSS	Ovary	ovary
32	chr5:112627000-112627400	Flanking Active TSS	Left Ventricle	heart
33	chr5:112627000-112627600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr5:112627000-112627600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr5:112627000-112628400	Enhancers	Fetal Muscle Leg	muscle
36	chr5:112627000-112629000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr5:112627200-112627400	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr5:112627200-112627400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr5:112627200-112627400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr5:112627200-112627400	Flanking Active TSS	Psoas Muscle	Psoas
41	chr5:112627200-112627600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
42	chr5:112627200-112628000	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr5:112627200-112628000	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr5:112627200-112628000	Weak transcription	Adipose Nuclei	Adipose
45	chr5:112627200-112628200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr5:112627200-112628200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr5:112627200-112628200	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr5:112627200-112628200	Weak transcription	NHEK	skin
49	chr5:112627200-112628600	Weak transcription	Lung	lung
50	chr5:112627200-112628800	Weak transcription	Aorta	Aorta

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