Variant report

Variant	rs4754200
Chromosome Location	chr11:107116078-107116079
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:107114259..107116985-chr11:107121608..107123484,2	K562	blood:

Extended variants
information (count: 104 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10749889	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10749892	0.81[AMR][1000 genomes]
rs10789591	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10789595	0.80[AMR][1000 genomes]
rs10789596	0.81[AMR][1000 genomes]
rs10890666	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10890668	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1352735	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1472078	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1490942	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1559669	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1808472	0.80[AMR][1000 genomes]
rs1817798	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1834330	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1844748	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1844750	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1863260	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1863261	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1907403	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1991197	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2017907	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2059462	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2098846	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2113926	0.81[AMR][1000 genomes]
rs2113927	0.81[AMR][1000 genomes]
rs2130823	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2194844	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2355841	0.81[AMR][1000 genomes]
rs2355842	0.81[AMR][1000 genomes]
rs2432869	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs2883480	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2883633	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs4265572	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs473520	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs4753787	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4754208	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4754212	0.81[AMR][1000 genomes]
rs478067	0.81[CHB][hapmap];0.93[JPT][hapmap]
rs501088	0.81[AMR][1000 genomes]
rs512574	1.00[ASW][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap];0.85[MEX][hapmap];0.80[AMR][1000 genomes]
rs525996	0.81[CHB][hapmap];0.92[JPT][hapmap]
rs541277	0.81[AMR][1000 genomes]
rs550882	0.80[AMR][1000 genomes]
rs551168	0.93[JPT][hapmap]
rs556528	0.85[JPT][hapmap]
rs557972	0.81[AMR][1000 genomes]
rs559269	0.93[JPT][hapmap]
rs574014	0.81[JPT][hapmap]
rs580913	0.81[CHB][hapmap];0.93[JPT][hapmap]
rs594772	0.81[AMR][1000 genomes]
rs602628	0.81[AMR][1000 genomes]
rs603487	0.81[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes]
rs604211	0.81[CHB][hapmap];0.93[JPT][hapmap]
rs607151	0.81[CHB][hapmap];0.84[JPT][hapmap];0.80[AMR][1000 genomes]
rs610203	0.80[AMR][1000 genomes]
rs615998	0.81[AMR][1000 genomes]
rs621677	0.81[CHB][hapmap];0.92[JPT][hapmap];0.80[AMR][1000 genomes]
rs639437	0.92[JPT][hapmap]
rs650699	0.81[CHB][hapmap];0.93[JPT][hapmap]
rs651620	0.81[CHB][hapmap];0.93[JPT][hapmap]
rs655005	0.80[JPT][hapmap]
rs6588950	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6588961	0.81[AMR][1000 genomes]
rs661889	0.85[CHD][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap]
rs682042	0.81[CHB][hapmap];0.93[JPT][hapmap]
rs682590	0.81[CHB][hapmap];0.93[JPT][hapmap];0.80[AMR][1000 genomes]
rs686806	1.00[ASW][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap]
rs7101699	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7102140	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7106065	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7108632	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7112390	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7115296	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7127931	0.84[AMR][1000 genomes]
rs7131186	0.81[AMR][1000 genomes]
rs7927069	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7931852	0.81[AMR][1000 genomes]
rs7932042	0.81[AMR][1000 genomes]
rs7932525	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7932991	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7935653	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7936346	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7938897	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7945258	0.82[AMR][1000 genomes]
rs7945936	0.84[AMR][1000 genomes]
rs7946110	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7946787	0.84[AMR][1000 genomes]
rs90623	0.80[AMR][1000 genomes]
rs962380	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531938	chr11:106760733-107156814	Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv898364	chr11:106944975-107285636	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv898365	chr11:106944975-107430300	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv898366	chr11:106944975-107433835	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv898367	chr11:106944975-107443420	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv898369	chr11:106958304-107443420	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv832260	chr11:106975094-107181795	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv556279	chr11:107006900-107186896	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1035911	chr11:107020991-107198181	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv898370	chr11:107027991-107430300	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv1040190	chr11:107045534-107175661	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv898371	chr11:107049968-107130964	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv898372	chr11:107049968-107433835	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	esv2760577	chr11:107112270-107128014	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
15	nsv1045881	chr11:107113815-107128014	Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4754200	CARD17	cis	cerebellum	SCAN
rs4754200	PDGFD	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:107115200-107116200	Weak transcription	HepG2	liver
2	chr11:107116000-107116200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr11:107116000-107116600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr11:107116000-107116600	Enhancers	K562	blood

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