Variant report

Variant	rs6880349
Chromosome Location	chr5:1829065-1829066
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:1827997..1830349-chr5:1831198..1833616,2	K562	blood:
2	chr5:1798421..1802098-chr5:1826976..1829813,3	K562	blood:
3	chr5:1811455..1813099-chr5:1828682..1831578,2	K562	blood:

Variant related genes	Relation type
ENSG00000145494	Chromatin interaction
ENSG00000171421	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10037336	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10045048	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10051882	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10058270	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10062133	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10070488	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10078791	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10085011	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10475110	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10475112	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10475113	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11505118	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11505119	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13361288	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16884830	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16901194	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28402979	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28573163	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28609097	1.00[ASN][1000 genomes]
rs2883061	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs464685	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs58926651	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59515251	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60876329	0.85[EUR][1000 genomes]
rs6555013	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6861074	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6861795	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6862138	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6862330	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6862520	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6864000	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6866992	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6875087	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6881273	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6881623	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6885220	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6888753	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6895439	0.80[AMR][1000 genomes]
rs6899016	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73732314	0.81[EUR][1000 genomes]
rs73734916	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73734940	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73734941	1.00[ASN][1000 genomes]
rs7707424	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7709350	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7711522	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7718031	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7723998	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7725178	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs924462	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9312955	0.81[EUR][1000 genomes];1.00[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	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	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
7	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
8	nsv596891	chr5:1822326-1880891	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv880647	chr5:1822326-1880891	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv881619	chr5:1822326-1886471	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv881557	chr5:1822326-1932463	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1821800-1831000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr5:1821800-1832000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr5:1822000-1830400	Weak transcription	Primary B cells from peripheral blood	blood
4	chr5:1822200-1830800	Weak transcription	HSMM	muscle
5	chr5:1822200-1831800	Weak transcription	HSMMtube	muscle
6	chr5:1822400-1829400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr5:1822400-1830000	Weak transcription	Fetal Lung	lung
8	chr5:1822400-1831600	Weak transcription	HMEC	breast
9	chr5:1822400-1833200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr5:1822600-1829400	Weak transcription	NH-A	brain
11	chr5:1822600-1831600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr5:1822800-1831200	Weak transcription	Osteobl	bone
13	chr5:1823000-1830000	Weak transcription	K562	blood
14	chr5:1824400-1829800	Weak transcription	HepG2	liver
15	chr5:1825000-1829400	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr5:1825000-1832400	Weak transcription	Brain Anterior Caudate	brain
17	chr5:1825000-1832800	Weak transcription	Brain Substantia Nigra	brain
18	chr5:1825200-1831600	Weak transcription	Brain Hippocampus Middle	brain
19	chr5:1825200-1832600	Weak transcription	Brain Angular Gyrus	brain
20	chr5:1825600-1831400	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr5:1825600-1832400	Weak transcription	Liver	Liver
22	chr5:1825800-1830400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr5:1825800-1831600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr5:1826200-1829200	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr5:1826200-1829400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr5:1826200-1831600	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr5:1826200-1832000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr5:1826400-1831200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr5:1826400-1831800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr5:1826600-1830800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr5:1826600-1831000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr5:1826600-1831600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr5:1826600-1833600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr5:1826800-1829400	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr5:1826800-1829600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr5:1826800-1829600	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr5:1826800-1830600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr5:1826800-1831200	Weak transcription	Primary T cells from cord blood	blood
39	chr5:1826800-1831800	Weak transcription	Fetal Intestine Small	intestine
40	chr5:1827000-1830600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr5:1827000-1831800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr5:1827000-1833400	Weak transcription	Left Ventricle	heart
43	chr5:1827000-1836800	Weak transcription	Gastric	stomach
44	chr5:1827200-1830600	Weak transcription	Fetal Brain Female	brain
45	chr5:1827200-1833200	Weak transcription	Brain Germinal Matrix	brain
46	chr5:1827600-1831400	Weak transcription	Hela-S3	cervix
47	chr5:1827600-1854000	Weak transcription	Right Atrium	heart
48	chr5:1827800-1829800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr5:1827800-1830800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr5:1827800-1830800	Weak transcription	NHLF	lung

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