Variant report

Variant	rs40109
Chromosome Location	chr5:61707641-61707642
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:61696503..61703698-chr5:61706632..61711868,15	MCF-7	breast:
2	chr5:61696900..61702493-chr5:61705289..61710261,23	K562	blood:
3	chr5:61697532..61701694-chr5:61703408..61710603,12	MCF-7	breast:
4	chr5:61705281..61708194-chr5:61728089..61730384,3	K562	blood:
5	chr5:61601533..61603969-chr5:61707379..61709702,2	K562	blood:

Variant related genes	Relation type
ENSG00000086200	Chromatin interaction
ENSG00000086189	Chromatin interaction
ENSG00000068796	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs13156073	0.91[ASN][1000 genomes]
rs13190153	0.85[ASN][1000 genomes]
rs153859	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs153860	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs153864	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs153866	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs153869	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs153873	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs173530	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs17382217	0.91[EUR][1000 genomes]
rs181784	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs190445	0.82[AMR][1000 genomes]
rs2272291	0.91[ASN][1000 genomes]
rs2441115	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs246198	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs246200	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2463079	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs247477	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs247480	0.88[ASN][1000 genomes]
rs247481	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs247484	0.82[ASN][1000 genomes]
rs255391	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs255392	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2650500	0.82[ASN][1000 genomes]
rs26619	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs26620	0.88[ASN][1000 genomes]
rs26626	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs26627	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs27090	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs32047	0.82[ASN][1000 genomes]
rs32148	0.82[AMR][1000 genomes]
rs32149	0.82[AMR][1000 genomes]
rs32156	0.82[AMR][1000 genomes]
rs32162	0.82[AMR][1000 genomes]
rs32170	0.82[AMR][1000 genomes]
rs32172	0.82[AMR][1000 genomes]
rs32173	0.82[AMR][1000 genomes]
rs32178	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs32180	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs32183	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs32184	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs32185	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs32189	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs35011	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs35012	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs35054	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35055	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35058	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs369624	0.82[AMR][1000 genomes]
rs3822487	0.85[ASN][1000 genomes]
rs40290	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs40579	0.82[AMR][1000 genomes]
rs417822	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs785665	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs785666	0.88[ASN][1000 genomes]
rs785667	0.88[ASN][1000 genomes]
rs814169	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024090	chr5:61258759-61921150	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2759345	chr5:61403138-61748912	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats 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 target site	31 gene(s)	inside rSNPs	diseases
3	nsv1020255	chr5:61451792-62031365	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1027539	chr5:61457762-62000008	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv1033578	chr5:61606610-61911153	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv1025145	chr5:61624735-61824265	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv1029708	chr5:61625813-61877628	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv881728	chr5:61630879-61857577	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	esv2757117	chr5:61649403-61748912	Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
10	nsv598348	chr5:61650843-61895124	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
11	esv35035	chr5:61657943-61792243	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:61700600-61707800	Weak transcription	Right Ventricle	heart
2	chr5:61700800-61707800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr5:61700800-61707800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr5:61700800-61707800	Weak transcription	Placenta	Placenta
5	chr5:61700800-61707800	Weak transcription	Stomach Mucosa	stomach
6	chr5:61701000-61707800	Weak transcription	Primary T cells from cord blood	blood
7	chr5:61701000-61707800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr5:61701000-61707800	Weak transcription	Hela-S3	cervix
9	chr5:61701000-61708000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr5:61701200-61707800	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr5:61701200-61707800	Weak transcription	NHEK	skin
12	chr5:61706800-61707800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr5:61707600-61707800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr5:61707600-61707800	Enhancers	Primary hematopoietic stem cells	blood
15	chr5:61707600-61707800	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr5:61707600-61707800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr5:61707600-61707800	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr5:61707600-61707800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr5:61707600-61707800	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr5:61707600-61707800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr5:61707600-61707800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr5:61707600-61707800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr5:61707600-61707800	Enhancers	Adipose Nuclei	Adipose
24	chr5:61707600-61707800	Enhancers	Liver	Liver
25	chr5:61707600-61707800	Enhancers	Brain Cingulate Gyrus	brain
26	chr5:61707600-61707800	Enhancers	Duodenum Mucosa	Duodenum
27	chr5:61707600-61707800	Enhancers	Fetal Heart	heart
28	chr5:61707600-61707800	Enhancers	Fetal Lung	lung
29	chr5:61707600-61707800	Enhancers	Fetal Muscle Leg	muscle
30	chr5:61707600-61707800	Enhancers	Rectal Mucosa Donor 29	rectum
31	chr5:61707600-61707800	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr5:61707600-61707800	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr5:61707600-61707800	Enhancers	Thymus	Thymus
34	chr5:61707600-61707800	Enhancers	Dnd41	blood
35	chr5:61707600-61707800	Enhancers	HUVEC	blood vessel
36	chr5:61707600-61707800	Enhancers	Monocytes-CD14+_RO01746	blood

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