Variant report

Variant	rs6852503
Chromosome Location	chr4:10579236-10579237
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1004325	0.86[TSI][hapmap]
rs1019124	0.85[CEU][hapmap]
rs10938855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11934521	0.85[CHB][hapmap]
rs11936679	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11938495	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11938610	0.87[EUR][1000 genomes]
rs12650414	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17383040	0.85[CHB][hapmap]
rs17383137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17467581	0.85[CHB][hapmap]
rs17467602	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17467609	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1966375	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1989245	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1990272	0.92[CEU][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2011545	0.86[TSI][hapmap]
rs2014303	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2079685	0.86[TSI][hapmap]
rs2098057	0.85[TSI][hapmap]
rs2302170	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2531194	0.85[TSI][hapmap]
rs2720352	0.88[TSI][hapmap]
rs2720354	0.88[TSI][hapmap]
rs2720371	0.85[TSI][hapmap]
rs2720372	0.85[TSI][hapmap]
rs2869470	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2904113	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35783374	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4697759	0.82[ASW][hapmap];0.92[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.93[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56325310	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61495782	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61795106	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61795107	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6448095	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6816045	0.90[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6818298	0.84[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6819450	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6840081	0.84[CEU][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6848730	0.85[GIH][hapmap];0.80[TSI][hapmap];0.83[EUR][1000 genomes]
rs73228220	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73228224	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs763677	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs7657440	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7665577	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7674488	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7683820	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7685040	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7685227	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs978591	0.88[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008649	chr4:9805223-10589802	Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6852503	GRPEL1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:10576000-10583000	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr4:10577200-10585600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr4:10577800-10579400	Enhancers	Primary B cells from cord blood	blood
4	chr4:10578200-10580000	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr4:10578200-10580000	Enhancers	Fetal Thymus	thymus
6	chr4:10578200-10581000	Enhancers	GM12878-XiMat	blood
7	chr4:10578400-10579400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr4:10578400-10579400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr4:10578400-10579400	Enhancers	Thymus	Thymus
10	chr4:10578600-10579600	Enhancers	Primary hematopoietic stem cells	blood
11	chr4:10578600-10579600	Enhancers	Fetal Brain Female	brain
12	chr4:10578600-10579600	Enhancers	Fetal Muscle Leg	muscle
13	chr4:10579000-10579400	Enhancers	Adipose Nuclei	Adipose
14	chr4:10579000-10584800	Weak transcription	Primary B cells from peripheral blood	blood
15	chr4:10579200-10579400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr4:10579200-10580000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr4:10579200-10585200	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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