Variant report

Variant	rs522277
Chromosome Location	chr1:120288333-120288334
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:120286920..120290208-chr1:120298529..120301740,3	K562	blood:
2	chr1:120261924..120264165-chr1:120287525..120289595,2	K562	blood:
3	chr1:120278483..120280232-chr1:120286168..120288570,2	K562	blood:
4	chr1:120286100..120288877-chr1:120290549..120293981,3	K562	blood:
5	chr1:120282346..120286075-chr1:120287322..120291391,4	K562	blood:

Variant related genes	Relation type
ENSG00000092621	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1441008	0.82[CHB][hapmap]
rs1441010	0.95[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs517237	0.82[CHD][hapmap]
rs518027	0.87[CEU][hapmap];0.94[GIH][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs543703	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.84[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs566864	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs590825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs591162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs593911	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs608358	0.86[CEU][hapmap];0.88[MEX][hapmap];0.81[TSI][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs610404	1.00[CEU][hapmap];0.87[CHB][hapmap];0.84[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs619167	0.82[CHD][hapmap]
rs627070	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs649733	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs651347	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs667246	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs689198	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv1000939	chr1:119983342-120471049	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv831204	chr1:120266449-120314091	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv831215	chr1:120266449-120448469	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	nsv428201	chr1:120267313-120697156	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	esv2757750	chr1:120267313-121226013	Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	esv2758965	chr1:120267313-121226013	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs522277	ILVBL	trans	parietal	SCAN
rs522277	ATP1A1	cis	parietal	SCAN
rs522277	VANGL1	cis	parietal	SCAN
rs522277	SPAG17	cis	cerebellum	SCAN
rs522277	CD58	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:120258600-120289200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:120263400-120291400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:120279200-120290600	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr1:120280400-120289400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:120282000-120293400	Weak transcription	Aorta	Aorta
6	chr1:120283600-120288600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr1:120285400-120288800	Weak transcription	HSMM	muscle
8	chr1:120285600-120292200	Weak transcription	Lung	lung
9	chr1:120285800-120289400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:120285800-120289600	Weak transcription	Ovary	ovary
11	chr1:120286000-120288600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr1:120286000-120289600	Weak transcription	Pancreas	Pancrea
13	chr1:120286000-120290000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr1:120286000-120290200	Weak transcription	NHLF	lung
15	chr1:120286200-120289200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:120286200-120289200	Weak transcription	Placenta	Placenta
17	chr1:120286400-120289200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:120286600-120289200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:120286600-120289200	Weak transcription	Gastric	stomach
20	chr1:120286600-120289200	Weak transcription	HMEC	breast
21	chr1:120286600-120289600	Enhancers	Liver	Liver
22	chr1:120286600-120289600	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr1:120286600-120291400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr1:120286800-120288400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:120286800-120288600	Weak transcription	Primary T cells from cord blood	blood
26	chr1:120286800-120288600	Enhancers	HepG2	liver
27	chr1:120286800-120289600	Weak transcription	Esophagus	oesophagus
28	chr1:120286800-120289800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:120286800-120289800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr1:120286800-120290800	Weak transcription	Adipose Nuclei	Adipose
31	chr1:120286800-120290800	Weak transcription	Colonic Mucosa	Colon
32	chr1:120286800-120290800	Weak transcription	Duodenum Mucosa	Duodenum
33	chr1:120286800-120290800	Weak transcription	Fetal Lung	lung
34	chr1:120286800-120297800	Weak transcription	Right Ventricle	heart
35	chr1:120286800-120302200	Weak transcription	Rectal Smooth Muscle	rectum
36	chr1:120286800-120310000	Weak transcription	Psoas Muscle	Psoas
37	chr1:120287000-120290800	Weak transcription	Spleen	Spleen
38	chr1:120287000-120301800	Weak transcription	Left Ventricle	heart
39	chr1:120287000-120308200	Weak transcription	Stomach Mucosa	stomach
40	chr1:120287200-120288800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr1:120287200-120288800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr1:120287200-120288800	Weak transcription	Brain Germinal Matrix	brain
43	chr1:120287200-120289200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr1:120287200-120289400	Weak transcription	NHEK	skin
45	chr1:120287200-120289600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr1:120287200-120290000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr1:120287200-120290000	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr1:120287200-120290000	Weak transcription	Hela-S3	cervix
49	chr1:120287200-120290400	Weak transcription	Fetal Heart	heart
50	chr1:120287200-120293400	Weak transcription	Right Atrium	heart

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