Variant report

Variant	rs613825
Chromosome Location	chr5:43022045-43022046
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:43015093..43022227-chr5:43063428..43069370,31	MCF-7	breast:
2	chr5:43007851..43010366-chr5:43021276..43023527,2	K562	blood:
3	chr5:43014739..43026335-chr5:43034830..43045515,33	MCF-7	breast:
4	chr5:43017275..43019485-chr5:43020964..43022856,2	MCF-7	breast:
5	chr5:43019686..43022766-chr5:43029707..43032686,3	K562	blood:

Variant related genes	Relation type
ENSG00000251131	Chromatin interaction
ENSG00000177738	Chromatin interaction
ENSG00000172262	Chromatin interaction
ENSG00000215068	Chromatin interaction
ENSG00000177721	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10064003	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10522	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10941604	0.87[ASN][1000 genomes]
rs10941605	0.87[ASN][1000 genomes]
rs11747435	0.87[ASN][1000 genomes]
rs11958008	0.87[ASN][1000 genomes]
rs12697439	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13169690	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13170208	0.94[ASN][1000 genomes]
rs13171133	0.85[ASN][1000 genomes]
rs13178479	0.94[ASN][1000 genomes]
rs13179934	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1542369	0.93[ASN][1000 genomes]
rs1574407	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs160709	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs186324	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs1902101	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2100473	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2124069	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs222060	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2247280	0.84[AMR][1000 genomes]
rs2253450	0.87[ASN][1000 genomes]
rs2329994	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329995	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2548334	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2548336	0.84[AFR][1000 genomes]
rs2548345	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2548349	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2548350	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2548353	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2548356	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2548373	0.85[AMR][1000 genomes]
rs2603295	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2603620	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2603634	0.85[AMR][1000 genomes]
rs2603636	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2603644	0.85[AFR][1000 genomes]
rs2603656	0.87[ASN][1000 genomes]
rs2882295	0.86[AFR][1000 genomes]
rs2924817	0.82[AMR][1000 genomes]
rs309909	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs309914	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs309921	0.80[AMR][1000 genomes]
rs309924	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs309925	0.80[AMR][1000 genomes]
rs309926	0.85[AMR][1000 genomes]
rs309927	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs309948	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs309950	0.84[AFR][1000 genomes]
rs309951	0.82[ASN][1000 genomes]
rs316395	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316396	0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs316400	0.88[ASN][1000 genomes]
rs316402	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs316403	0.83[ASN][1000 genomes]
rs316404	0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs316408	0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs316414	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs316416	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs316419	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316422	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4033115	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4092293	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4092294	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4296812	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs515970	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs543569	0.88[ASN][1000 genomes]
rs565761	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs643307	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6451660	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6451661	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6451662	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6875214	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs724430	0.93[ASN][1000 genomes]
rs768441	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7715065	0.89[ASN][1000 genomes]
rs9292862	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
2	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
3	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
4	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
5	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
6	nsv534185	chr5:42804840-43067088	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	165 gene(s)	inside rSNPs	diseases
7	nsv1029288	chr5:42928085-43047323	Flanking Bivalent TSS/Enh Active TSS Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	120 gene(s)	inside rSNPs	diseases
8	nsv968169	chr5:42956713-43043472	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	116 gene(s)	inside rSNPs	diseases
9	nsv1024636	chr5:42959979-43295782	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
10	nsv537739	chr5:42959979-43295782	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
11	nsv880447	chr5:42967215-43030798	Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
12	nsv881640	chr5:42978644-43028221	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	94 gene(s)	inside rSNPs	diseases
13	nsv880415	chr5:42978644-43030798	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	94 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43020200-43034800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:43020800-43024000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:43020800-43030000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr5:43020800-43033600	Weak transcription	NH-A	brain
5	chr5:43020800-43033800	Weak transcription	NHLF	lung
6	chr5:43020800-43034000	Weak transcription	Pancreas	Pancrea
7	chr5:43020800-43034200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr5:43020800-43034400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr5:43020800-43037400	Weak transcription	HSMM	muscle
10	chr5:43020800-43038400	Weak transcription	Spleen	Spleen
11	chr5:43021000-43022400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr5:43021000-43022400	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr5:43021000-43029000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr5:43021000-43030400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr5:43021000-43032600	Weak transcription	HUVEC	blood vessel
16	chr5:43021200-43038600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr5:43021400-43034400	Weak transcription	Primary B cells from cord blood	blood
18	chr5:43021600-43034200	Weak transcription	Primary B cells from peripheral blood	blood
19	chr5:43021600-43034400	Weak transcription	NHDF-Ad	bronchial
20	chr5:43021600-43034600	Weak transcription	Hela-S3	cervix
21	chr5:43021800-43022400	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr5:43021800-43029000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr5:43021800-43029000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr5:43021800-43029200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr5:43021800-43029200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr5:43021800-43030400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr5:43021800-43034400	Weak transcription	Dnd41	blood
28	chr5:43021800-43034600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr5:43022000-43027000	Weak transcription	HepG2	liver
30	chr5:43022000-43027600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr5:43022000-43036400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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