Variant report

Variant	rs6594700
Chromosome Location	chr5:112657404-112657405
allele	C/T
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	RAD21	chr5:112656932-112657434	SK-N-SH	brain:	n/a	n/a
2	RAD21	chr5:112656941-112657413	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112628328..112630254-chr5:112656025..112657722,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232633	TF binding region

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10036581	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10057210	0.84[ASN][1000 genomes]
rs10067046	1.00[ASW][hapmap];0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.90[MKK][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs10072511	0.88[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs10076501	1.00[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1038918	0.87[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs10900684	0.88[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.82[ASN][1000 genomes]
rs11241200	0.88[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];0.83[ASN][1000 genomes]
rs11748642	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11948072	1.00[CEU][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13153071	0.88[CEU][hapmap];0.81[CHB][hapmap];0.82[CHD][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.82[ASN][1000 genomes]
rs1517206	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1517210	0.83[CEU][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap]
rs164251	0.82[JPT][hapmap]
rs1845290	0.83[CEU][hapmap]
rs1850408	0.84[ASN][1000 genomes]
rs2165928	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2416310	0.88[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs255856	0.83[CEU][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap]
rs27566	0.83[CEU][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap]
rs3857435	0.83[CEU][hapmap];0.82[GIH][hapmap]
rs4108702	0.81[CHD][hapmap];0.92[MEX][hapmap]
rs423089	0.82[JPT][hapmap]
rs459428	0.82[JPT][hapmap]
rs461034	0.93[JPT][hapmap]
rs463216	0.87[JPT][hapmap]
rs465898	0.87[JPT][hapmap]
rs4705812	0.88[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap];0.84[ASN][1000 genomes]
rs4705813	0.80[AMR][1000 genomes]
rs485210	0.83[MEX][hapmap]
rs492346	0.83[MEX][hapmap]
rs6594711	0.83[CEU][hapmap]
rs6869097	0.83[CEU][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes]
rs6873400	0.86[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs6873755	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6875238	0.80[AMR][1000 genomes]
rs6879612	0.80[AMR][1000 genomes]
rs6894434	1.00[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7702120	0.83[CEU][hapmap];0.82[JPT][hapmap]
rs7722276	0.83[MEX][hapmap]
rs7735247	0.82[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs882755	1.00[YRI][hapmap]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6594700	YTHDC2	cis	parietal	SCAN
rs6594700	LILRP2	trans	parietal	SCAN
rs6594700	YTHDC2	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112648800-112666600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr5:112653000-112673600	Weak transcription	Fetal Kidney	kidney
3	chr5:112655000-112657600	Enhancers	Liver	Liver
4	chr5:112655800-112658600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr5:112655800-112658800	Weak transcription	Placenta	Placenta
6	chr5:112656000-112666200	Weak transcription	HMEC	breast
7	chr5:112656200-112661200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr5:112656600-112666600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr5:112657400-112669200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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