Variant report

Variant	rs1004439
Chromosome Location	chr17:16841924-16841925
allele	A/G
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	POLR2A	chr17:16841704-16842306	GM12891	blood:	n/a	n/a
2	POLR2A	chr17:16841754-16842240	GM12891	blood:	n/a	n/a
3	CTCF	chr17:16841910-16842047	GM19239	blood:	n/a	n/a
4	POLR2A	chr17:16841814-16842175	GM12878	blood:	n/a	n/a
5	POLR2A	chr17:16841790-16842195	GM12891	blood:	n/a	n/a
6	STAT5A	chr17:16837390-16842245	GM12878	blood:	n/a	n/a
7	POLR2A	chr17:16834953-16843440	GM12878	blood:	n/a	n/a
8	POLR2A	chr17:16841240-16842318	GM12892	blood:	n/a	n/a
9	STAT5A	chr17:16841497-16842003	GM12878	blood:	n/a	n/a
10	POLR2A	chr17:16841832-16842208	GM12878	blood:	n/a	n/a
11	POLR2A	chr17:16841769-16842269	GM12892	blood:	n/a	n/a
12	POLR2A	chr17:16841701-16842897	GM12892	blood:	n/a	n/a
13	POLR2A	chr17:16841768-16842201	GM12892	blood:	n/a	n/a
14	POLR2A	chr17:16841818-16842234	GM12878	blood:	n/a	n/a
15	POLR2A	chr17:16840620-16844926	GM12878	blood:	n/a	n/a
16	POLR2A	chr17:16841850-16842214	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:16839251..16842055-chr17:16843809..16846753,2	K562	blood:

Variant related genes	Relation type
TBC1D27	TF binding region
ENSG00000240505	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11078356	0.84[CEU][hapmap]
rs11649835	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11650590	1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11650981	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11651187	0.81[CEU][hapmap]
rs11651352	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11652811	0.85[AMR][1000 genomes]
rs11652843	1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs11654431	0.83[CEU][hapmap]
rs17793572	0.84[CEU][hapmap]
rs35380019	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4343329	0.89[CEU][hapmap];0.82[TSI][hapmap]
rs4517836	1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs4985720	1.00[YRI][hapmap]
rs55635506	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55770108	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56035746	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56092540	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56369903	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56396775	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56408153	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62065417	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62065418	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62065421	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62065423	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62065424	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62065425	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62065426	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62065427	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62065429	0.80[EUR][1000 genomes]
rs62065430	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6502540	0.80[AMR][1000 genomes]
rs6502545	1.00[YRI][hapmap]
rs7209074	0.80[AMR][1000 genomes]
rs7225344	0.88[CEU][hapmap]
rs7504096	1.00[YRI][hapmap]
rs8072293	0.94[GIH][hapmap];0.84[MEX][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes]
rs8081126	0.84[CEU][hapmap]
rs9889948	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058448	chr17:16389870-16926287	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	esv2753951	chr17:16660721-16848750	Enhancers Bivalent Enhancer Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	esv2755100	chr17:16660721-16848750	Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv833379	chr17:16683585-16859539	Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv1055688	chr17:16800788-16868860	Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1058863	chr17:16812121-16943780	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv543227	chr17:16812121-16943780	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv907726	chr17:16821204-16875636	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1004439	LOC96597	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16834800-16842800	Weak transcription	Spleen	Spleen
2	chr17:16837000-16842000	Weak transcription	Brain Anterior Caudate	brain
3	chr17:16837200-16844400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr17:16838400-16843000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr17:16840000-16843800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr17:16840200-16842000	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr17:16840800-16847400	Strong transcription	GM12878-XiMat	blood
8	chr17:16841000-16846600	Strong transcription	Primary B cells from peripheral blood	blood
9	chr17:16841400-16842600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
10	chr17:16841400-16843000	Enhancers	Fetal Thymus	thymus
11	chr17:16841600-16842400	Enhancers	Fetal Muscle Leg	muscle
12	chr17:16841800-16842400	Flanking Active TSS	Dnd41	blood
13	chr17:16841800-16844200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr17:16841800-16844400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links