Variant report

Variant	rs7727449
Chromosome Location	chr5:112771824-112771825
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF263	chr5:112771751-112772349	HEK293-T-REx	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112771582..112773208-chr5:112822674..112824229,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-YTHDC2-1	chr5:112771263-112772871	ENSG00000232633.3

Variant related genes	Relation type
TSSK1B	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10036300	0.84[JPT][hapmap];0.94[YRI][hapmap]
rs10037429	0.89[YRI][hapmap]
rs11744710	0.89[YRI][hapmap]
rs11744737	0.89[YRI][hapmap]
rs11948187	0.82[YRI][hapmap]
rs11948437	0.84[YRI][hapmap]
rs11949669	0.84[YRI][hapmap]
rs1517210	0.87[CHB][hapmap];0.84[CHD][hapmap]
rs1593953	0.84[ASN][1000 genomes]
rs164251	0.87[CHB][hapmap]
rs164252	0.92[YRI][hapmap]
rs182988	0.84[YRI][hapmap]
rs1845290	0.87[CHB][hapmap]
rs2416282	0.80[MEX][hapmap]
rs255856	0.87[CHB][hapmap];0.84[CHD][hapmap];0.80[MEX][hapmap]
rs26985	0.94[CHB][hapmap];0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs26987	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs26988	0.85[AMR][1000 genomes]
rs27566	0.87[CHB][hapmap];0.83[CHD][hapmap];0.80[MEX][hapmap]
rs34075952	0.80[ASN][1000 genomes]
rs348939	0.89[YRI][hapmap]
rs3857435	0.94[CHB][hapmap];0.80[MEX][hapmap]
rs3857437	0.82[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs3906371	0.83[GIH][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap]
rs423089	1.00[CHB][hapmap]
rs4324667	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4398627	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.97[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs459428	0.94[CHB][hapmap]
rs461034	0.86[CHB][hapmap]
rs463216	0.87[CHB][hapmap]
rs465898	0.87[CHB][hapmap]
rs466564	0.94[CHB][hapmap];0.85[AMR][1000 genomes]
rs6594711	0.94[CHB][hapmap]
rs675353	0.94[CHB][hapmap];0.86[CHD][hapmap]
rs6869097	0.87[CHB][hapmap]
rs7702120	0.80[CHB][hapmap]
rs7713348	0.80[ASN][1000 genomes]
rs7730802	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7727449	YTHDC2	cis	cerebellum	SCAN
rs7727449	YTHDC2	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112762000-112786000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:112764400-112779200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:112764600-112786400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr5:112764800-112786800	Weak transcription	NHEK	skin
5	chr5:112770200-112773800	Enhancers	Fetal Stomach	stomach
6	chr5:112770400-112772200	Enhancers	Fetal Muscle Leg	muscle
7	chr5:112770400-112783400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr5:112770600-112772000	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr5:112770600-112773600	Enhancers	Fetal Heart	heart
10	chr5:112770600-112786800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr5:112770800-112772000	Enhancers	Right Atrium	heart
12	chr5:112770800-112773000	Enhancers	Fetal Brain Male	brain
13	chr5:112770800-112773600	Enhancers	Fetal Lung	lung
14	chr5:112771000-112772000	Enhancers	Fetal Muscle Trunk	muscle
15	chr5:112771200-112772000	Enhancers	Left Ventricle	heart
16	chr5:112771400-112772000	Enhancers	Brain Hippocampus Middle	brain
17	chr5:112771400-112772200	Enhancers	Fetal Brain Female	brain

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