Variant report

Variant	rs6897545
Chromosome Location	chr5:1619135-1619136
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:1555041..1557212-chr5:1618820..1621277,2	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10043201	0.83[AMR][1000 genomes]
rs10052477	0.84[ASN][1000 genomes]
rs10061756	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10062417	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10064943	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10475075	0.84[ASN][1000 genomes]
rs1048186	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11958585	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28556838	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7710273	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7734433	0.81[ASN][1000 genomes]
rs7734561	0.83[ASN][1000 genomes]
rs9312899	0.83[ASN][1000 genomes]
rs9312909	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv880740	chr5:1468287-1671200	Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	49 gene(s)	inside rSNPs	diseases
3	nsv881554	chr5:1468287-1696932	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	49 gene(s)	inside rSNPs	diseases
4	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
5	nsv881096	chr5:1503610-1671200	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
6	nsv596879	chr5:1519079-1624351	Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
7	nsv10657	chr5:1544428-1633373	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv596885	chr5:1552255-1624351	Bivalent Enhancer Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv964815	chr5:1608931-1639317	Strong transcription Active TSS Weak transcription Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv880390	chr5:1612612-1653418	Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	esv3423630	chr5:1618178-1619193	Weak transcription Strong transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
12	esv3450297	chr5:1618250-1619298	Weak transcription Strong transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:21)

SNP	Gene	Cis/trans	Tissue	Source
rs6897545	CTD-2012J19.1	cis	Nerve Tibial	GTEx
rs6897545	RP11-43F13.1	cis	Thyroid	GTEx
rs6897545	LOC728613	Cis_1M	lymphoblastoid	RTeQTL
rs6897545	RP11-43F13.1	cis	Skin Sun Exposed Lower leg	GTEx
rs6897545	CTD-2012J19.1	cis	Esophagus Muscularis	GTEx
rs6897545	CTD-2012J19.1	cis	Thyroid	GTEx
rs6897545	LOC728613///PDCD6	Cis_1M	lymphoblastoid	RTeQTL
rs6897545	RP11-43F13.1	cis	Muscle Skeletal	GTEx
rs6897545	RP11-43F13.1	cis	Artery Tibial	GTEx
rs6897545	CTD-2012J19.1	cis	lung	GTEx
rs6897545	CTD-2012J19.1	cis	Adipose Subcutaneous	GTEx
rs6897545	RP11-43F13.1	cis	lung	GTEx
rs6897545	CTD-2012J19.1	cis	Artery Tibial	GTEx
rs6897545	CTD-2012J19.1	cis	Skin Sun Exposed Lower leg	GTEx
rs6897545	RP11-43F13.1	cis	Whole Blood	GTEx
rs6897545	RP11-43F13.1	cis	Heart Left Ventricle	GTEx
rs6897545	CTD-2012J19.1	cis	Muscle Skeletal	GTEx
rs6897545	RP11-43F13.1	cis	Adipose Subcutaneous	GTEx
rs6897545	RP11-43F13.1	cis	Artery Aorta	GTEx
rs6897545	CTD-2012J19.1	cis	Stomach	GTEx
rs6897545	RP11-43F13.1	cis	Esophagus Muscularis	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1595000-1626600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr5:1595000-1634000	Weak transcription	Stomach Mucosa	stomach
3	chr5:1595200-1632800	Weak transcription	Brain Angular Gyrus	brain
4	chr5:1595200-1632800	Weak transcription	Right Ventricle	heart
5	chr5:1595400-1619200	Weak transcription	GM12878-XiMat	blood
6	chr5:1595400-1619400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr5:1595400-1633200	Weak transcription	Primary B cells from cord blood	blood
8	chr5:1595400-1633200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr5:1595400-1633200	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr5:1595400-1633200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr5:1597600-1619200	Weak transcription	Fetal Brain Female	brain
12	chr5:1597600-1621400	Weak transcription	Brain Substantia Nigra	brain
13	chr5:1597600-1621800	Weak transcription	Ovary	ovary
14	chr5:1597600-1626400	Weak transcription	Adipose Nuclei	Adipose
15	chr5:1597600-1632600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr5:1597600-1632800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr5:1597600-1632800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr5:1597600-1633000	Weak transcription	Brain Hippocampus Middle	brain
19	chr5:1601400-1632800	Weak transcription	Hela-S3	cervix
20	chr5:1601800-1620600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr5:1606200-1633200	Weak transcription	Brain Anterior Caudate	brain
22	chr5:1607600-1621000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr5:1607600-1626600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr5:1607800-1623800	Weak transcription	Fetal Muscle Leg	muscle
25	chr5:1608000-1620600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr5:1608000-1624200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr5:1608400-1626400	Weak transcription	Pancreas	Pancrea
28	chr5:1608600-1620800	Weak transcription	Brain Germinal Matrix	brain
29	chr5:1608800-1624600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr5:1608800-1632800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr5:1608800-1633800	Weak transcription	Fetal Lung	lung
32	chr5:1609200-1633200	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr5:1609200-1633200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr5:1609400-1619200	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr5:1609400-1619400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr5:1609600-1633600	Weak transcription	Left Ventricle	heart
37	chr5:1609800-1626400	Weak transcription	HepG2	liver
38	chr5:1610000-1621600	Weak transcription	Fetal Kidney	kidney
39	chr5:1610000-1624400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr5:1610000-1633400	Weak transcription	Colonic Mucosa	Colon
41	chr5:1610600-1632800	Weak transcription	NHEK	skin
42	chr5:1610600-1633200	Weak transcription	Colon Smooth Muscle	Colon
43	chr5:1611000-1619200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr5:1611200-1624000	Weak transcription	Esophagus	oesophagus
45	chr5:1611800-1633800	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr5:1612200-1624400	Weak transcription	Aorta	Aorta
47	chr5:1612800-1621200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr5:1613200-1633200	Weak transcription	HSMMtube	muscle
49	chr5:1613800-1621000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr5:1613800-1633800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links