Variant report

Variant	rs522534
Chromosome Location	chr1:179891092-179891093
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:179890721..179893462-chr1:179922578..179925183,2	MCF-7	breast:
2	chr1:179889909..179891977-chr1:179899561..179901875,2	K562	blood:
3	chr1:179885300..179888007-chr1:179889040..179891794,2	MCF-7	breast:
4	chr1:179890511..179892011-chr1:179902778..179905230,2	MCF-7	breast:
5	chr1:179885633..179888323-chr1:179889442..179891149,2	K562	blood:
6	chr1:179889749..179892017-chr1:179923918..179925424,2	MCF-7	breast:
7	chr1:179850249..179852659-chr1:179890266..179891877,2	MCF-7	breast:
8	chr1:179890847..179892932-chr1:179926143..179929567,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000272906	Chromatin interaction
ENSG00000143337	Chromatin interaction
ENSG00000260360	Chromatin interaction
ENSG00000135837	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1144575	0.93[ASN][1000 genomes]
rs1148812	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1148815	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12062341	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12062383	0.88[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1281378	0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1281408	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1281411	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1281412	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1281413	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1281428	0.91[ASN][1000 genomes]
rs1281429	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1281430	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1281432	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1298477	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1298479	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1300068	0.88[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2007148	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2245425	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2249346	0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2762858	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2777908	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2777909	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2777917	0.90[AMR][1000 genomes]
rs2794582	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2794583	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs474258	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs475233	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs475434	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs479094	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs480377	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs480498	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs486906	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs501300	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs505789	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs505837	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs507603	0.94[ASN][1000 genomes]
rs514421	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs518774	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs530369	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs530854	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs531814	0.82[EUR][1000 genomes]
rs538512	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs547776	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs549650	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs553830	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs555270	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs555526	0.95[ASN][1000 genomes]
rs589780	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs599185	0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs600046	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs600553	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs605807	0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs609521	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs612215	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs644412	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6657364	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv429947	chr1:179790518-179925104	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179867400-179897200	Weak transcription	Stomach Mucosa	stomach
2	chr1:179868200-179891600	Strong transcription	Primary B cells from peripheral blood	blood
3	chr1:179868200-179891800	Strong transcription	Primary T cells fromperipheralblood	blood
4	chr1:179868600-179891600	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr1:179868600-179892000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:179869200-179891600	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr1:179869400-179891400	Strong transcription	Liver	Liver
8	chr1:179873400-179891400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr1:179875200-179891800	Strong transcription	Primary B cells from cord blood	blood
10	chr1:179876000-179891200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:179877000-179891600	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr1:179881000-179891400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr1:179881800-179891200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr1:179882000-179891600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr1:179886400-179891600	Strong transcription	Duodenum Mucosa	Duodenum
16	chr1:179886800-179891200	Strong transcription	GM12878-XiMat	blood
17	chr1:179887200-179893400	Weak transcription	Pancreas	Pancrea
18	chr1:179887200-179897200	Weak transcription	Fetal Intestine Small	intestine
19	chr1:179887400-179891400	Weak transcription	Psoas Muscle	Psoas
20	chr1:179887400-179891600	Weak transcription	Spleen	Spleen
21	chr1:179887400-179892800	Weak transcription	Gastric	stomach
22	chr1:179887400-179894600	Weak transcription	HSMMtube	muscle
23	chr1:179887400-179897200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:179887400-179897600	Weak transcription	Aorta	Aorta
25	chr1:179887400-179898600	Weak transcription	Right Ventricle	heart
26	chr1:179887400-179899200	Weak transcription	Small Intestine	intestine
27	chr1:179887400-179900600	Weak transcription	Ovary	ovary
28	chr1:179887400-179901600	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr1:179887600-179895200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr1:179887600-179899400	Weak transcription	K562	blood
31	chr1:179887800-179892000	Weak transcription	Fetal Heart	heart
32	chr1:179887800-179892200	Weak transcription	Colonic Mucosa	Colon
33	chr1:179887800-179893000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr1:179887800-179899400	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr1:179888000-179891600	Weak transcription	NH-A	brain
36	chr1:179888000-179894600	Weak transcription	HMEC	breast
37	chr1:179888200-179892200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr1:179888200-179892400	Weak transcription	Fetal Brain Female	brain
39	chr1:179888600-179892000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr1:179888600-179892000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:179888600-179892200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr1:179888600-179892800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr1:179888600-179895200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr1:179888600-179895600	Weak transcription	NHLF	lung
45	chr1:179888600-179897200	Weak transcription	Esophagus	oesophagus
46	chr1:179888600-179897200	Weak transcription	Fetal Intestine Large	intestine
47	chr1:179888600-179899400	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr1:179888800-179892000	Weak transcription	Fetal Lung	lung
49	chr1:179888800-179892400	Weak transcription	Primary hematopoietic stem cells	blood
50	chr1:179888800-179894400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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