Variant report

Variant	rs985604
Chromosome Location	chr10:91927403-91927404
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFATC1	chr10:91927350-91927840	GM12878	blood:	n/a	n/a
2	ATF2	chr10:91927400-91927804	GM12878	blood:	n/a	n/a
3	NFATC1	chr10:91927355-91927824	GM12878	blood:	n/a	n/a
4	MEF2C	chr10:91927290-91927781	GM12878	blood:	n/a	chr10:91927619-91927627 chr10:91927475-91927490
5	RELA	chr10:91926933-91927742	GM18505	blood:	n/a	chr10:91927095-91927104 chr10:91927095-91927104
6	MEF2A	chr10:91926840-91927765	GM12878	blood:	n/a	chr10:91926961-91926970 chr10:91926958-91926973 chr10:91926954-91926975 chr10:91926959-91926973 chr10:91926960-91926971 chr10:91927619-91927627 chr10:91926954-91926975 chr10:91927475-91927490 chr10:91926954-91926975
7	MEF2A	chr10:91927246-91927821	GM12878	blood:	n/a	chr10:91927619-91927627 chr10:91927475-91927490
8	FOXM1	chr10:91926920-91927824	GM12878	blood:	n/a	n/a
9	FOS	chr10:91927333-91927830	MCF10A-Er-Src	breast:	n/a	chr10:91927619-91927628
10	NFIC	chr10:91926811-91927869	GM12878	blood:	n/a	n/a
11	TBL1XR1	chr10:91927356-91927677	GM12878	blood:	n/a	n/a
12	RELA	chr10:91926940-91927768	GM12891	blood:	n/a	chr10:91927095-91927104 chr10:91927095-91927104
13	FOS	chr10:91927392-91927821	MCF10A-Er-Src	breast:	n/a	chr10:91927619-91927628
14	NFIC	chr10:91927332-91927860	GM12878	blood:	n/a	n/a
15	RUNX3	chr10:91927401-91927787	GM12878	blood:	n/a	n/a
16	RELA	chr10:91926933-91927763	GM12892	blood:	n/a	chr10:91927095-91927104 chr10:91927095-91927104
17	MTA3	chr10:91926953-91927791	GM12878	blood:	n/a	n/a
18	BATF	chr10:91927387-91927750	GM12878	blood:	n/a	n/a
19	IKZF1	chr10:91927035-91927774	GM12878	blood:	n/a	n/a
20	ATF2	chr10:91927258-91927862	GM12878	blood:	n/a	n/a
21	FOS	chr10:91927384-91928372	MCF10A-Er-Src	breast:	n/a	chr10:91928204-91928212 chr10:91927619-91927628 chr10:91928204-91928212 chr10:91928203-91928214 chr10:91928204-91928211
22	RELA	chr10:91926918-91927742	GM12878	blood:	n/a	chr10:91927095-91927104 chr10:91927095-91927104
23	CEBPB	chr10:91927401-91927883	HCT-116	colon:	n/a	chr10:91927539-91927550
24	RUNX3	chr10:91926841-91927791	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
RN7SKP143	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10881759	0.81[ASN][1000 genomes]
rs1329154	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17091294	0.93[JPT][hapmap]
rs1925823	0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs4142854	0.81[ASN][1000 genomes]
rs6583692	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs985602	0.93[JPT][hapmap]
rs985603	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs999901	0.93[JPT][hapmap]
rs999902	0.93[JPT][hapmap]
rs999903	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043571	chr10:91568555-92036154	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv551874	chr10:91570211-92036154	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv949678	chr10:91589048-92016474	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv895883	chr10:91610601-92195828	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv1039731	chr10:91645718-92198264	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv540743	chr10:91645718-92198264	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv467430	chr10:91681344-92297943	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv551875	chr10:91681344-92297943	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv895884	chr10:91861413-91959144	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	esv3375393	chr10:91880933-92243227	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv895885	chr10:91912493-91988922	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv467431	chr10:91922383-91942219	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
13	nsv551878	chr10:91922383-91942219	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs985604	LIPA	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:91923800-91935000	Weak transcription	Esophagus	oesophagus
2	chr10:91924000-91930800	Weak transcription	Primary B cells from cord blood	blood
3	chr10:91924400-91928000	Weak transcription	NHLF	lung
4	chr10:91927000-91927800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr10:91927000-91927800	Enhancers	Osteobl	bone
6	chr10:91927000-91928200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr10:91927000-91928200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr10:91927200-91927600	Active TSS	GM12878-XiMat	blood
9	chr10:91927200-91928400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr10:91927400-91928200	Enhancers	HMEC	breast

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