Variant report

Variant	rs2987532
Chromosome Location	chr13:49547975-49547976
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ZNF274	chr13:49547775-49548277	NT2-D1	testis:	n/a	n/a
2	ZNF274	chr13:49547618-49549717	GM08714	blood:	n/a	n/a
3	POLR2A	chr13:49547351-49552910	MCF10A-Er-Src	breast:	n/a	n/a
4	ZNF274	chr13:49546640-49549948	K562	blood:	n/a	n/a
5	SETDB1	chr13:49547817-49549721	U2OS	brain:	n/a	n/a
6	SETDB1	chr13:49547579-49549442	K562	blood:	n/a	n/a
7	ZNF274	chr13:49547644-49548359	K562	blood:	n/a	n/a
8	KAP1	chr13:49547806-49549182	K562	blood:	n/a	n/a
9	ZNF274	chr13:49547787-49548924	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:49546080..49548216-chr13:49556766..49558384,2	MCF-7	breast:
2	chr13:49511991..49514025-chr13:49547058..49549833,2	K562	blood:
3	chr13:49547950..49551813-chr13:49821954..49825536,3	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CAB39L-4	chr13:49546319-49550047	NONHSAT033727

No data

Variant related genes	Relation type
FNDC3A	TF binding region
ENSG00000102543	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1359066	0.91[CEU][hapmap];0.91[CHB][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs1407827	0.91[CEU][hapmap];0.91[CHB][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs1407829	0.91[CEU][hapmap];0.91[CHB][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs1928109	0.82[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1928110	0.84[EUR][1000 genomes]
rs1937180	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1937181	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap]
rs1983805	0.90[CEU][hapmap];0.91[CHB][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs2026029	0.91[CEU][hapmap];0.91[CHB][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs2146748	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs2149498	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2181539	0.83[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap]
rs2183095	0.88[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2407265	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2407266	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2897633	0.95[CEU][hapmap];0.91[CHB][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs2987528	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2987535	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2994377	0.83[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes]
rs2994378	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.82[AMR][1000 genomes]
rs2994379	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2994380	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2994381	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3012116	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3012117	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3012118	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3012121	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3012127	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3012133	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3012135	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3012136	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4142065	0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs4530025	0.95[CEU][hapmap];0.87[CHB][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs4942795	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4942796	0.91[CEU][hapmap];0.91[CHB][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4942798	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4942799	0.91[CEU][hapmap];0.91[CHB][hapmap];0.87[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs4942800	0.91[CEU][hapmap];0.87[CHB][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap]
rs6561491	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6561496	0.83[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap]
rs6561497	0.83[ASW][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.93[MKK][hapmap]
rs7139854	0.84[EUR][1000 genomes]
rs720627	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs728075	0.86[CEU][hapmap];0.91[CHB][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7322842	0.89[ASN][1000 genomes]
rs7325026	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7328000	0.82[EUR][1000 genomes]
rs7329291	0.91[CEU][hapmap];0.91[CHB][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7331917	0.82[AMR][1000 genomes]
rs7333097	0.91[CHB][hapmap]
rs7338529	0.91[CEU][hapmap];0.91[CHB][hapmap]
rs7983885	0.91[CEU][hapmap];0.91[CHB][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs7986624	0.82[CEU][hapmap];0.91[CHB][hapmap];0.85[EUR][1000 genomes]
rs7987258	0.82[CEU][hapmap];0.91[MEX][hapmap]
rs7988168	0.83[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7989175	0.91[CHB][hapmap]
rs7994910	0.91[CEU][hapmap];0.91[CHB][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes]
rs7995616	0.91[CEU][hapmap];0.91[CHB][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap]
rs7997118	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7998359	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7999513	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9316426	0.83[ASW][hapmap];0.91[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9316427	0.82[ASN][1000 genomes]
rs9316428	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs9316429	0.91[CHB][hapmap]
rs9526518	0.95[CEU][hapmap];0.86[CHB][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9526520	0.90[CHB][hapmap];0.84[EUR][1000 genomes]
rs9526521	0.98[GIH][hapmap];0.83[EUR][1000 genomes]
rs9535126	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535133	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9535136	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs9535145	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap]
rs9535146	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs9535147	0.91[CEU][hapmap];0.91[CHB][hapmap]
rs9535149	0.95[CEU][hapmap];0.91[CHB][hapmap]
rs9535154	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap]
rs9535155	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap]
rs9535156	0.91[CEU][hapmap];0.91[CHB][hapmap]
rs9562866	0.83[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9568150	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap]
rs9568151	0.95[CEU][hapmap];0.91[CHB][hapmap]
rs9568154	0.90[CHB][hapmap]
rs9591235	0.81[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	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1034	chr13:49526761-49572727	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv455882	chr13:49531551-49679157	Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv561593	chr13:49531551-49679157	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	esv1792084	chr13:49536705-49549571	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv1793883	chr13:49543723-49789164	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2987532	SERP2	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49546600-49549000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr13:49546800-49549000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
3	chr13:49546800-49549400	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr13:49547400-49548800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr13:49547600-49548000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
6	chr13:49547600-49549200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
7	chr13:49547800-49549000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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