Variant report

Variant	rs2520276
Chromosome Location	chr7:107129404-107129405
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:107129283..107132125-chr7:107690846..107692465,2	K562	blood:
2	chr7:107123396..107125120-chr7:107128160..107130150,2	K562	blood:
3	chr7:107121684..107125374-chr7:107125563..107129660,8	K562	blood:
4	chr7:107115877..107118056-chr7:107127031..107129912,2	K562	blood:

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1015410	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs1018869	0.84[EUR][1000 genomes]
rs1024401	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10244871	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs10245210	0.93[EUR][1000 genomes]
rs10260250	0.88[CEU][hapmap];0.86[CHB][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.91[TSI][hapmap]
rs10267978	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10276321	0.84[EUR][1000 genomes]
rs10953538	0.93[EUR][1000 genomes]
rs11761775	0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];0.82[ASN][1000 genomes]
rs12532304	0.93[EUR][1000 genomes]
rs12534598	0.95[CHB][hapmap];0.86[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.82[ASN][1000 genomes]
rs12668615	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1468335	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1858889	0.97[EUR][1000 genomes]
rs2237667	0.89[CEU][hapmap];0.81[CHB][hapmap];0.91[JPT][hapmap]
rs2250410	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs2253856	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs2283042	0.82[EUR][1000 genomes]
rs2520257	0.87[EUR][1000 genomes]
rs2520258	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2520259	0.85[EUR][1000 genomes]
rs2520262	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2520266	0.85[EUR][1000 genomes]
rs2520270	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2520272	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs2520278	0.97[EUR][1000 genomes]
rs2520279	1.00[CEU][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes]
rs2701678	0.82[JPT][hapmap]
rs2701679	0.82[JPT][hapmap]
rs2712186	0.85[EUR][1000 genomes]
rs2712188	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs2712192	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2712194	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2712203	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2712213	0.85[EUR][1000 genomes]
rs2712217	0.86[EUR][1000 genomes]
rs2712223	0.83[EUR][1000 genomes]
rs2712225	0.82[EUR][1000 genomes]
rs28410326	0.96[EUR][1000 genomes]
rs3779496	0.89[AFR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4727682	0.92[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.83[AFR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4730243	0.85[EUR][1000 genomes]
rs4730244	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs60490203	0.84[EUR][1000 genomes]
rs62483724	0.85[EUR][1000 genomes]
rs6466172	0.87[EUR][1000 genomes]
rs6466174	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6945488	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6962433	0.86[EUR][1000 genomes]
rs6968804	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs711442	0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];0.81[ASN][1000 genomes]
rs7786186	0.97[EUR][1000 genomes]
rs7787113	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs7791955	0.96[CEU][hapmap];0.94[EUR][1000 genomes]
rs7805630	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1825788	chr7:106897237-107136320	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv1024793	chr7:106900877-107170312	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	esv1832266	chr7:106961882-107136320	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv1033979	chr7:107003734-107877761	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
5	nsv1019963	chr7:107033342-107188641	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv539052	chr7:107033342-107188641	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv1028571	chr7:107114479-107299723	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv539053	chr7:107114479-107299723	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv482365	chr7:107122401-107271861	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2520276	COG5	cis	cerebellum	SCAN
rs2520276	MLL5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:107035800-107133000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr7:107090800-107146000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr7:107091000-107145800	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr7:107098800-107132600	Weak transcription	Primary B cells from cord blood	blood
5	chr7:107112800-107145800	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr7:107115400-107132800	Weak transcription	Primary T cells from cord blood	blood
7	chr7:107115600-107135200	Weak transcription	Left Ventricle	heart
8	chr7:107120000-107145600	Weak transcription	Right Ventricle	heart
9	chr7:107120200-107135200	Weak transcription	Fetal Intestine Small	intestine
10	chr7:107122000-107147000	Weak transcription	HSMM	muscle
11	chr7:107123200-107155800	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr7:107123600-107166200	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr7:107126600-107135600	Weak transcription	Pancreas	Pancrea
14	chr7:107126600-107145600	Weak transcription	Adipose Nuclei	Adipose
15	chr7:107126800-107131000	Weak transcription	Fetal Heart	heart
16	chr7:107126800-107184800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr7:107127400-107175400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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