Variant report

Variant	rs519472
Chromosome Location	chr1:10492405-10492406
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:10457794..10460664-chr1:10487844..10492697,5	K562	blood:
2	chr1:10490607..10494447-chr1:10532445..10535163,5	K562	blood:
3	chr1:10488008..10492443-chr1:10531123..10534892,8	K562	blood:
4	chr1:10489993..10493018-chr1:10531254..10535234,5	MCF-7	breast:
5	chr1:10490864..10493248-chr1:10508230..10510272,2	K562	blood:
6	chr1:10489448..10493967-chr1:10494423..10498103,7	K562	blood:
7	chr1:10457881..10459696-chr1:10491385..10493588,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160049	Chromatin interaction
ENSG00000251503	Chromatin interaction
ENSG00000241563	Chromatin interaction
ENSG00000142655	Chromatin interaction
ENSG00000142657	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10746494	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11121579	0.80[ASN][1000 genomes]
rs1203122	0.87[EUR][1000 genomes]
rs1307485	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1307487	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1750349	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1760664	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2483684	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2781233	0.86[EUR][1000 genomes]
rs36013615	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs475549	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs481571	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs491880	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs505141	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs517241	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs520964	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs522029	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs522280	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs524150	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs528713	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs579398	0.92[ASN][1000 genomes]
rs583515	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs585703	0.95[ASN][1000 genomes]
rs586096	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs586223	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs597441	0.85[EUR][1000 genomes]
rs628462	0.82[ASN][1000 genomes]
rs632690	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs634358	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs643400	0.89[EUR][1000 genomes]
rs649101	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs649639	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs655271	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs663864	0.80[ASN][1000 genomes]
rs666583	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs667366	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs672606	0.86[EUR][1000 genomes]
rs678850	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs681448	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs681495	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[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	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv2764192	chr1:10383734-10594186	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1003498	chr1:10445928-10607351	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer 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	26 gene(s)	inside rSNPs	diseases
7	nsv998731	chr1:10464176-10607351	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10491400-10493000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:10491400-10493600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:10491400-10504600	Weak transcription	Lung	lung
4	chr1:10491400-10519000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:10491400-10521000	Weak transcription	Ovary	ovary
6	chr1:10491400-10521200	Weak transcription	Aorta	Aorta
7	chr1:10491600-10492600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:10491600-10492600	Enhancers	Brain Angular Gyrus	brain
9	chr1:10491600-10492600	Enhancers	Fetal Heart	heart
10	chr1:10491600-10492800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:10491600-10492800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:10491600-10492800	Enhancers	Fetal Brain Male	brain
13	chr1:10491600-10492800	Weak transcription	Fetal Lung	lung
14	chr1:10491600-10493000	Enhancers	GM12878-XiMat	blood
15	chr1:10491600-10493200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr1:10491600-10494000	Weak transcription	Fetal Kidney	kidney
17	chr1:10491600-10496800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:10491600-10500000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr1:10491600-10500400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:10491600-10504600	Weak transcription	HSMMtube	muscle
21	chr1:10491600-10508000	Weak transcription	Colon Smooth Muscle	Colon
22	chr1:10491600-10510200	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr1:10491600-10510200	Weak transcription	Gastric	stomach
24	chr1:10491600-10510400	Weak transcription	Right Atrium	heart
25	chr1:10491600-10511000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr1:10491600-10511000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr1:10491600-10511200	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr1:10491600-10516200	Weak transcription	HMEC	breast
29	chr1:10491600-10517800	Weak transcription	Primary T cells from cord blood	blood
30	chr1:10491600-10518000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr1:10491600-10518000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr1:10491600-10519200	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr1:10491600-10521200	Weak transcription	Brain Substantia Nigra	brain
34	chr1:10491600-10521200	Weak transcription	Left Ventricle	heart
35	chr1:10491600-10521200	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr1:10491600-10521200	Weak transcription	Spleen	Spleen
37	chr1:10491600-10521400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr1:10491800-10492600	Enhancers	Fetal Intestine Small	intestine
39	chr1:10491800-10492800	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr1:10491800-10492800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr1:10491800-10492800	Weak transcription	Fetal Muscle Trunk	muscle
42	chr1:10491800-10492800	Weak transcription	K562	blood
43	chr1:10491800-10493000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr1:10491800-10493200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:10491800-10493200	Weak transcription	Liver	Liver
46	chr1:10491800-10493200	Weak transcription	Fetal Brain Female	brain
47	chr1:10491800-10493400	Weak transcription	Primary B cells from peripheral blood	blood
48	chr1:10491800-10493800	Enhancers	Duodenum Mucosa	Duodenum
49	chr1:10491800-10494200	Enhancers	Fetal Intestine Large	intestine
50	chr1:10491800-10494200	Enhancers	Pancreas	Pancrea

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