Variant report

Variant	rs41340151
Chromosome Location	chr4:10593863-10593864
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	chr4:10584329..10586994-chr4:10592921..10595277,2	K562	blood:

Extended variants
information (count: 81 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10027001	0.83[TSI][hapmap]
rs11934521	0.87[CEU][hapmap];0.82[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[MKK][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11938495	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12502030	0.87[CEU][hapmap]
rs17382947	0.82[CEU][hapmap];0.81[YRI][hapmap];0.84[EUR][1000 genomes]
rs17382963	0.85[CEU][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17383005	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs17383033	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17383040	0.87[CEU][hapmap];0.82[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17383095	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17383130	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17383186	0.82[CHB][hapmap]
rs17467476	0.84[EUR][1000 genomes]
rs17467581	0.87[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17467602	0.85[ASN][1000 genomes]
rs17467609	0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17467937	0.83[TSI][hapmap]
rs1989245	0.85[ASN][1000 genomes]
rs1990272	0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2014303	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2302170	0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2869470	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs35265323	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4323097	0.87[CEU][hapmap]
rs4697759	0.82[CHB][hapmap]
rs4697772	0.86[CEU][hapmap]
rs55804861	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55878273	0.87[EUR][1000 genomes]
rs56325310	0.85[ASN][1000 genomes]
rs58442828	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58728006	0.86[EUR][1000 genomes]
rs59203169	0.87[EUR][1000 genomes]
rs61495782	0.87[ASN][1000 genomes]
rs61795106	0.87[ASN][1000 genomes]
rs61795107	0.85[ASN][1000 genomes]
rs6448068	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6811270	0.80[MEX][hapmap];0.83[TSI][hapmap]
rs6816045	0.85[ASN][1000 genomes]
rs6818298	0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs6819450	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs6837268	0.81[EUR][1000 genomes]
rs6845149	0.80[MEX][hapmap]
rs6846414	0.87[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6848059	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6855648	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6856210	0.87[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73228207	0.86[EUR][1000 genomes]
rs73228210	0.86[EUR][1000 genomes]
rs73228212	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73228224	0.85[ASN][1000 genomes]
rs73228227	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73228228	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73228236	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7439618	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs763677	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7657440	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7659607	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7674488	0.87[ASN][1000 genomes]
rs7683820	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7685040	0.83[ASN][1000 genomes]
rs7685227	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7694378	0.87[ASW][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.80[MEX][hapmap];0.90[MKK][hapmap];0.87[TSI][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7696635	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1000587	chr4:9805223-10610752	Flanking Active TSS Enhancers Genic enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
2	nsv537022	chr4:9805223-10610752	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
3	nsv1003454	chr4:9805223-10710990	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
4	nsv537023	chr4:9805223-10710990	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
5	nsv1004801	chr4:9814720-10674528	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
6	nsv537024	chr4:9814720-10674528	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
7	nsv931483	chr4:9814721-10716463	Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
8	nsv1009972	chr4:9903566-10710990	Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
9	nsv537027	chr4:9903566-10710990	Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
10	nsv1010620	chr4:9937123-10686682	Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
11	nsv530280	chr4:9947818-10940041	Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	66 gene(s)	inside rSNPs	diseases
12	nsv869057	chr4:10013411-10875454	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
13	nsv997936	chr4:10040713-11009045	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
14	nsv593727	chr4:10397327-10694991	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
15	nsv517971	chr4:10399068-10893253	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
16	nsv878694	chr4:10407572-10783606	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
17	nsv878697	chr4:10501373-10831866	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
18	nsv878698	chr4:10536544-10632404	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs41340151	GRPEL1	cis	cerebellum	SCAN
rs41340151	SORCS2	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:10591400-10595000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr4:10592200-10606800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr4:10593200-10598000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr4:10593200-10598000	Weak transcription	HSMM	muscle
5	chr4:10593200-10598000	Weak transcription	NH-A	brain
6	chr4:10593200-10598000	Weak transcription	Osteobl	bone
7	chr4:10593200-10602800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr4:10593200-10606800	Weak transcription	NHLF	lung
9	chr4:10593200-10607200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr4:10593400-10598400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr4:10593400-10598400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr4:10593400-10598800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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