Variant report

Variant	rs62388633
Chromosome Location	chr6:1525835-1525836
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:1522639..1525978-chr6:1527169..1529799,4	K562	blood:
2	chr6:1525690..1526651-chr6:1641283..1642196,7	MCF-7	breast:
3	chr6:1525299..1527850-chr6:1532850..1536880,3	K562	blood:
4	chr6:1525690..1526651-chr6:1641283..1642196,5	MCF-7	breast:
5	chr6:1481665..1482260-chr6:1525723..1526611,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FOXC1-6	chr6:1523967-1527642	NONHSAT106509
2	lnc-FOXC1-6	chr6:1524730-1528405	NONHSAT106510

No data

Variant related genes	Relation type
ENSG00000272279	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs12523787	1.00[ASN][1000 genomes]
rs12525317	1.00[ASN][1000 genomes]
rs12530463	1.00[ASN][1000 genomes]
rs13191308	1.00[ASN][1000 genomes]
rs13197210	1.00[ASN][1000 genomes]
rs13201037	1.00[ASN][1000 genomes]
rs13203964	1.00[ASN][1000 genomes]
rs13209162	1.00[ASN][1000 genomes]
rs13210401	1.00[ASN][1000 genomes]
rs13212794	1.00[ASN][1000 genomes]
rs17828568	1.00[ASN][1000 genomes]
rs2015974	1.00[ASN][1000 genomes]
rs2317967	1.00[ASN][1000 genomes]
rs2317968	1.00[ASN][1000 genomes]
rs2745610	1.00[ASN][1000 genomes]
rs2816224	1.00[ASN][1000 genomes]
rs2816225	1.00[ASN][1000 genomes]
rs34114087	1.00[ASN][1000 genomes]
rs34779492	1.00[ASN][1000 genomes]
rs35040319	1.00[ASN][1000 genomes]
rs35412353	1.00[ASN][1000 genomes]
rs35694654	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35793648	1.00[ASN][1000 genomes]
rs361530	1.00[ASN][1000 genomes]
rs4367416	1.00[ASN][1000 genomes]
rs55821127	1.00[ASN][1000 genomes]
rs62388638	1.00[ASN][1000 genomes]
rs62388641	1.00[ASN][1000 genomes]
rs62390562	1.00[ASN][1000 genomes]
rs6596831	1.00[ASN][1000 genomes]
rs71550060	1.00[ASN][1000 genomes]
rs71550061	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs910016	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024111	chr6:1231850-1730146	Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1021924	chr6:1254891-1736995	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv538082	chr6:1254891-1736995	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv917248	chr6:1365437-1627813	Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv1034039	chr6:1427061-1691837	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv538088	chr6:1427061-1691837	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv530548	chr6:1441421-2351608	Weak transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
8	nsv883373	chr6:1443099-1529135	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv1027393	chr6:1446300-1692019	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
10	nsv538089	chr6:1446300-1692019	Bivalent Enhancer Weak transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
11	nsv883374	chr6:1454334-1558449	Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv1016859	chr6:1460020-1645819	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
13	nsv883375	chr6:1478613-1558449	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv1021878	chr6:1486780-1545589	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv538090	chr6:1486780-1545589	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs62388633	RP11-157J24.2	cis	Esophagus Mucosa	GTEx
rs62388633	RP11-157J24.2	cis	Adipose Subcutaneous	GTEx
rs62388633	RP11-157J24.2	cis	Esophagus Muscularis	GTEx
rs62388633	RP11-157J24.2	cis	Skin Sun Exposed Lower leg	GTEx
rs62388633	RP11-157J24.2	cis	lung	GTEx
rs62388633	RP11-157J24.2	cis	Thyroid	GTEx
rs62388633	RP11-157J24.2	cis	Muscle Skeletal	GTEx
rs62388633	RP11-157J24.2	cis	Artery Tibial	GTEx

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:1523800-1528000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr6:1524000-1527000	Enhancers	Brain Substantia Nigra	brain
3	chr6:1524600-1526400	Weak transcription	Esophagus	oesophagus
4	chr6:1524600-1526400	Weak transcription	Lung	lung
5	chr6:1524600-1526600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr6:1524600-1526600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr6:1524600-1526600	Weak transcription	Psoas Muscle	Psoas
8	chr6:1524600-1526800	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr6:1524600-1527000	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr6:1524600-1527000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr6:1524600-1527000	Weak transcription	Right Atrium	heart
12	chr6:1524600-1527000	Weak transcription	HMEC	breast
13	chr6:1524800-1526000	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr6:1524800-1526200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr6:1524800-1526400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr6:1524800-1526400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr6:1524800-1526600	Enhancers	Brain Anterior Caudate	brain
18	chr6:1524800-1526600	Enhancers	Brain Cingulate Gyrus	brain
19	chr6:1524800-1526600	Enhancers	Brain Hippocampus Middle	brain
20	chr6:1524800-1526600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr6:1524800-1526600	Weak transcription	Colon Smooth Muscle	Colon
22	chr6:1524800-1527000	Weak transcription	Fetal Kidney	kidney
23	chr6:1524800-1527000	Weak transcription	Ovary	ovary
24	chr6:1524800-1527000	Weak transcription	Spleen	Spleen
25	chr6:1524800-1527000	Weak transcription	Osteobl	bone
26	chr6:1524800-1528000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr6:1524800-1528000	Enhancers	Fetal Brain Male	brain
28	chr6:1524800-1528000	Enhancers	Fetal Muscle Leg	muscle
29	chr6:1524800-1528200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr6:1524800-1531400	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr6:1524800-1531600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
32	chr6:1524800-1531800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr6:1524800-1532200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr6:1525000-1526200	Weak transcription	Adipose Nuclei	Adipose
35	chr6:1525000-1526200	Weak transcription	Fetal Thymus	thymus
36	chr6:1525000-1526600	Weak transcription	Primary T cells from cord blood	blood
37	chr6:1525000-1526600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr6:1525000-1527000	Weak transcription	Gastric	stomach
39	chr6:1525000-1527000	Weak transcription	Pancreas	Pancrea
40	chr6:1525000-1527200	Weak transcription	Duodenum Mucosa	Duodenum
41	chr6:1525000-1529000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr6:1525000-1529200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr6:1525000-1530800	Enhancers	Primary T cells fromperipheralblood	blood
44	chr6:1525000-1531000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr6:1525000-1532200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr6:1525200-1526200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr6:1525200-1526400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr6:1525200-1527600	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr6:1525200-1527800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr6:1525200-1528000	Enhancers	Fetal Lung	lung

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