Variant report

Variant	rs4657477
Chromosome Location	chr1:165736175-165736176
allele	C/T
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:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:165735886..165744990-chr1:165791702..165805629,42	K562	blood:
2	chr1:165734875..165737199-chr1:165810836..165813345,2	K562	blood:
3	chr1:165736117..165742504-chr1:165795129..165799551,11	MCF-7	breast:
4	chr1:165733730..165736417-chr1:165798667..165800425,2	K562	blood:
5	chr1:165734862..165736387-chr1:165795496..165797680,2	K562	blood:
6	chr1:165735066..165739781-chr1:165794447..165799093,13	MCF-7	breast:
7	chr1:165735880..165737855-chr1:165863441..165866125,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000143183	Chromatin interaction
ENSG00000143179	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10800135	1.00[JPT][hapmap]
rs10800153	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800154	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10800155	1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10918274	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12133745	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12403369	1.00[JPT][hapmap]
rs12691499	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12691500	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1547725	0.91[CEU][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]
rs2251768	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs2790049	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2790052	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2790053	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2814463	0.83[ASN][1000 genomes]
rs2814466	1.00[JPT][hapmap]
rs2814471	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28504591	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4233408	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4537525	1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4603103	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656461	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657471	1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4657472	0.83[ASN][1000 genomes]
rs4657474	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4657475	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657476	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426936	0.80[AMR][1000 genomes]
rs6660601	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6662839	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668108	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668885	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6696454	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71628393	0.83[ASN][1000 genomes]
rs7518099	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7524755	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7528177	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7555523	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2756102	chr1:165652342-165877342	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1011720	chr1:165669589-165802516	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv518886	chr1:165714187-165741646	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4657477	MAEL	cis	cerebellum	SCAN
rs4657477	ARHGAP30	cis	parietal	SCAN
rs4657477	NDUFS2	cis	cerebellum	SCAN
rs4657477	ADCY10	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165687600-165737600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:165694600-165736800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr1:165711200-165736200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:165712200-165737000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:165712600-165737000	Weak transcription	Colonic Mucosa	Colon
6	chr1:165713600-165737000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:165721800-165736600	Weak transcription	Stomach Mucosa	stomach
8	chr1:165721800-165737000	Weak transcription	Fetal Brain Male	brain
9	chr1:165721800-165737000	Weak transcription	Fetal Heart	heart
10	chr1:165721800-165737000	Weak transcription	Right Atrium	heart
11	chr1:165721800-165737200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr1:165721800-165737600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:165722600-165736800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:165723000-165736800	Weak transcription	Spleen	Spleen
15	chr1:165723200-165736800	Weak transcription	Colon Smooth Muscle	Colon
16	chr1:165726400-165736800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:165726800-165736800	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr1:165726800-165737000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:165727000-165736800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:165727800-165737000	Weak transcription	Psoas Muscle	Psoas
21	chr1:165727800-165737600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:165729200-165737200	Weak transcription	Brain Substantia Nigra	brain
23	chr1:165730200-165736800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:165730200-165736800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:165730200-165736800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:165730400-165736600	Strong transcription	HSMM	muscle
27	chr1:165730400-165736800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr1:165730400-165736800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr1:165730600-165736600	Strong transcription	Hela-S3	cervix
30	chr1:165731200-165736800	Weak transcription	Gastric	stomach
31	chr1:165732200-165736600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
32	chr1:165732200-165736800	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr1:165732200-165736800	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr1:165732200-165736800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr1:165732200-165737000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr1:165732200-165737000	Strong transcription	Fetal Thymus	thymus
37	chr1:165732600-165736800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:165732600-165736800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr1:165732600-165737000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
40	chr1:165732600-165737200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr1:165732800-165736200	Strong transcription	Stomach Smooth Muscle	stomach
42	chr1:165732800-165736400	Strong transcription	Thymus	Thymus
43	chr1:165732800-165736600	Strong transcription	Osteobl	bone
44	chr1:165732800-165736800	Genic enhancers	Duodenum Mucosa	Duodenum
45	chr1:165732800-165737000	Strong transcription	Fetal Muscle Trunk	muscle
46	chr1:165732800-165737400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr1:165733000-165736800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr1:165733000-165737000	Strong transcription	Fetal Muscle Leg	muscle
49	chr1:165733000-165737200	Weak transcription	Rectal Smooth Muscle	rectum
50	chr1:165733200-165736400	Weak transcription	HepG2	liver

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