Variant report

Variant	rs11959430
Chromosome Location	chr5:89985363-89985364
allele	G/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	POLR2A	chr5:89984374-89986991	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:89984568..89985530-chr5:90079262..90080117,5	MCF-7	breast:
2	chr5:89985219..89986790-chr5:90677102..90678990,2	K562	blood:

Variant related genes	Relation type
GPR98	TF binding region
ENSG00000113369	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10080113	1.00[CEU][hapmap]
rs16868974	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16869015	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2203825	1.00[CEU][hapmap]
rs4283827	0.93[EUR][1000 genomes]
rs57252870	0.86[EUR][1000 genomes]
rs57255621	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57363721	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59411130	0.86[EUR][1000 genomes]
rs60470187	0.86[EUR][1000 genomes]
rs6865858	0.86[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6868367	0.84[AFR][1000 genomes]
rs6886668	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs6891645	1.00[CEU][hapmap]
rs73175203	0.93[EUR][1000 genomes]
rs73175215	0.93[EUR][1000 genomes]
rs73175221	0.93[EUR][1000 genomes]
rs73175282	0.93[EUR][1000 genomes]
rs73177403	0.86[EUR][1000 genomes]
rs73177407	0.86[EUR][1000 genomes]
rs73177409	0.86[EUR][1000 genomes]
rs73181664	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73181676	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73193228	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73193232	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73193236	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73193259	0.93[EUR][1000 genomes]
rs7706469	0.84[AFR][1000 genomes]
rs7714597	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7720923	0.84[AFR][1000 genomes]
rs7721331	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7721378	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432750	chr5:89410113-90137144	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv432751	chr5:89457044-90090444	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
4	nsv933668	chr5:89854253-89999672	Strong transcription Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
5	nsv531965	chr5:89886550-90145002	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
6	nsv1029970	chr5:89940489-89986831	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
7	nsv1032225	chr5:89940489-89999954	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
8	nsv1025391	chr5:89943364-89995164	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
9	nsv537805	chr5:89943364-89995164	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
10	nsv882367	chr5:89956991-90209824	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
11	nsv934323	chr5:89968158-90111853	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
12	nsv1015449	chr5:89968626-90219398	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89936800-89994200	Weak transcription	Brain Germinal Matrix	brain
2	chr5:89950400-90033400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr5:89964400-89993400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr5:89964600-89994800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr5:89965000-89993600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr5:89967200-89992000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:89972000-89985600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr5:89979200-90002600	Weak transcription	Brain Anterior Caudate	brain
9	chr5:89981800-89986200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr5:89981800-89992000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr5:89982000-89985600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr5:89982000-89985800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr5:89982000-89985800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr5:89982000-89986200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr5:89982000-89986200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr5:89982000-89986400	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr5:89982000-89986400	Weak transcription	K562	blood
18	chr5:89982000-89989800	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr5:89982000-90004600	Weak transcription	Fetal Brain Female	brain
20	chr5:89984200-89991800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr5:89985000-89994600	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr5:89985200-89986200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr5:89985200-89991400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:89985200-89993000	Strong transcription	HUES64 Cell Line	embryonic stem cell

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