Variant report

Variant	rs61740119
Chromosome Location	chr5:89949651-89949652
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:89948021..89949895-chr5:89950501..89953146,2	MCF-7	breast:
2	chr5:89921820..89923590-chr5:89949531..89951597,2	K562	blood:
3	chr5:89945551..89949827-chr5:89965829..89969902,5	K562	blood:

Variant related genes	Relation type
ENSG00000164199	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12108970	1.00[AMR][1000 genomes]
rs12109253	1.00[AMR][1000 genomes]
rs1504986	1.00[AMR][1000 genomes]
rs1504997	1.00[AMR][1000 genomes]
rs16868834	1.00[AMR][1000 genomes]
rs16868842	1.00[AMR][1000 genomes]
rs16868848	1.00[AMR][1000 genomes]
rs16868851	1.00[AMR][1000 genomes]
rs16868853	1.00[AMR][1000 genomes]
rs16868854	1.00[AMR][1000 genomes]
rs41304890	1.00[AMR][1000 genomes]
rs56926055	1.00[AMR][1000 genomes]
rs73179766	1.00[AMR][1000 genomes]
rs73179768	1.00[AMR][1000 genomes]
rs73179771	1.00[AMR][1000 genomes]
rs73179774	1.00[AMR][1000 genomes]
rs73179777	1.00[AMR][1000 genomes]
rs73179793	1.00[AMR][1000 genomes]
rs73181603	1.00[AMR][1000 genomes]
rs73181604	1.00[AMR][1000 genomes]
rs73181609	1.00[AMR][1000 genomes]
rs73181619	1.00[AMR][1000 genomes]
rs73181634	1.00[AMR][1000 genomes]
rs73181640	1.00[AMR][1000 genomes]
rs73181642	1.00[AMR][1000 genomes]
rs73181647	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73181653	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	nsv933161	chr5:89939500-89954066	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89918000-89950600	Weak transcription	Pancreas	Pancrea
2	chr5:89936600-89951000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:89936800-89951000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr5:89936800-89994200	Weak transcription	Brain Germinal Matrix	brain
5	chr5:89941400-89957400	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr5:89941600-89951600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr5:89941600-89954200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr5:89941800-89957600	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr5:89942800-89950200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr5:89944800-89956600	Weak transcription	Fetal Brain Male	brain
11	chr5:89945400-89951800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr5:89945800-89950400	Strong transcription	H1 Cell Line	embryonic stem cell
13	chr5:89946800-89950000	Genic enhancers	K562	blood
14	chr5:89948000-89950200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr5:89948000-89955400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:89948000-89955800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr5:89948400-89950800	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr5:89948600-89949800	Strong transcription	H9 Cell Line	embryonic stem cell
19	chr5:89948600-89950200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr5:89948600-89950200	Strong transcription	Fetal Brain Female	brain
21	chr5:89948600-89950800	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr5:89949000-89950400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr5:89949600-89951400	Weak transcription	Brain Anterior Caudate	brain
24	chr5:89949600-89954600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr5:89949600-89964000	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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