Variant report

Variant	rs6864000
Chromosome Location	chr5:1820557-1820558
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:1798514..1801939-chr5:1819696..1823981,5	MCF-7	breast:
2	chr5:1820025..1823818-chr5:1823864..1826357,3	K562	blood:
3	chr5:1814461..1816981-chr5:1818018..1821210,3	MCF-7	breast:
4	chr5:1818595..1823818-chr5:1824144..1826436,4	K562	blood:
5	chr5:1819853..1822198-chr5:1823585..1825204,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171421	Chromatin interaction
ENSG00000145494	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10037336	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10045048	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10051882	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10058270	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10061246	1.00[CHB][hapmap]
rs10062133	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10070488	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10078791	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10085011	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10085096	1.00[CHB][hapmap]
rs10085130	1.00[CHB][hapmap]
rs10474728	1.00[CEU][hapmap]
rs10475110	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10475112	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10475113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10475114	1.00[CEU][hapmap]
rs11505118	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11505119	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13361288	1.00[CEU][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16884830	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16901194	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28402979	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28573163	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28609097	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2883061	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41347149	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.92[YRI][hapmap]
rs464685	0.96[EUR][1000 genomes]
rs58926651	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59515251	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60876329	0.92[EUR][1000 genomes]
rs6555013	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6861074	1.00[CEU][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6861795	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6862138	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6862330	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6862520	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6866992	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6875087	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6880349	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6881273	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6881623	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6885220	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6888753	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6891921	1.00[CHB][hapmap]
rs6895439	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6899016	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73732314	0.88[EUR][1000 genomes]
rs73734916	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73734940	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73734941	1.00[ASN][1000 genomes]
rs7707424	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7709350	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7711522	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7718031	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7723998	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7725178	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs924462	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9312955	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933805	chr5:1450724-1941619	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv817407	chr5:1495354-2191460	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
3	nsv1034552	chr5:1658338-1856553	Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
4	nsv537606	chr5:1658338-1856553	Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
5	nsv869236	chr5:1719263-2259100	Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
6	nsv1024133	chr5:1736691-1826510	Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Enhancers Genic enhancers 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	40 gene(s)	inside rSNPs	diseases
7	nsv537609	chr5:1736691-1826510	Genic enhancers Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
8	nsv461911	chr5:1820557-1855301	Strong transcription Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
9	nsv596890	chr5:1820557-1855301	Enhancers Strong transcription Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1802200-1827800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr5:1802800-1821800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr5:1802800-1821800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr5:1802800-1822000	Strong transcription	Primary B cells from peripheral blood	blood
5	chr5:1802800-1822800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr5:1802800-1823000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr5:1802800-1823600	Strong transcription	Primary B cells from cord blood	blood
8	chr5:1802800-1825000	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr5:1802800-1825800	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr5:1802800-1826400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr5:1802800-1828400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr5:1803000-1822400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr5:1803000-1822400	Strong transcription	A549	lung
14	chr5:1803000-1822600	Strong transcription	Placenta	Placenta
15	chr5:1803000-1822800	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr5:1803000-1822800	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr5:1803000-1822800	Strong transcription	Osteobl	bone
18	chr5:1803000-1823800	Strong transcription	Fetal Thymus	thymus
19	chr5:1803000-1825000	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr5:1803000-1825000	Strong transcription	Rectal Mucosa Donor 29	rectum
21	chr5:1803000-1825600	Strong transcription	Liver	Liver
22	chr5:1803000-1826000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr5:1803000-1826200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr5:1803000-1826200	Strong transcription	Adipose Nuclei	Adipose
25	chr5:1803000-1826600	Strong transcription	Fetal Muscle Trunk	muscle
26	chr5:1803000-1826800	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr5:1803000-1827200	Strong transcription	Fetal Brain Female	brain
28	chr5:1803000-1828000	Strong transcription	Stomach Smooth Muscle	stomach
29	chr5:1803200-1821800	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr5:1803200-1822600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr5:1803200-1823000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr5:1803200-1825600	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr5:1803200-1825800	Strong transcription	Duodenum Mucosa	Duodenum
34	chr5:1803200-1826800	Strong transcription	Primary T cells from cord blood	blood
35	chr5:1803400-1821600	Strong transcription	Fetal Stomach	stomach
36	chr5:1803400-1822800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr5:1803400-1823600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr5:1803600-1823600	Strong transcription	Hela-S3	cervix
39	chr5:1803600-1826800	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr5:1803800-1822200	Strong transcription	HepG2	liver
41	chr5:1804000-1825000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr5:1804200-1822200	Strong transcription	Brain Germinal Matrix	brain
43	chr5:1804200-1823000	Strong transcription	K562	blood
44	chr5:1804200-1824600	Weak transcription	Fetal Brain Male	brain
45	chr5:1804400-1821600	Strong transcription	GM12878-XiMat	blood
46	chr5:1804600-1821600	Strong transcription	Spleen	Spleen
47	chr5:1808600-1821800	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr5:1808600-1825800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr5:1808800-1825000	Strong transcription	Brain Anterior Caudate	brain
50	chr5:1808800-1826200	Strong transcription	Primary T cells fromperipheralblood	blood

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