Variant report

Variant	rs1281413
Chromosome Location	chr1:179826030-179826031
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179820647..179822358-chr1:179825151..179827760,2	K562	blood:
2	chr1:179823204..179826152-chr1:179845562..179847449,3	K562	blood:
3	chr1:179824032..179826930-chr1:179846026..179848626,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000169905	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1014394	0.84[EUR][1000 genomes]
rs1144575	0.93[ASN][1000 genomes]
rs1148812	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1148815	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1148817	0.82[EUR][1000 genomes]
rs12062341	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12062383	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1281378	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1281408	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1281410	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1281411	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1281412	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1281428	0.97[ASN][1000 genomes]
rs1281429	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1281430	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1281432	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1298477	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1298479	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1300068	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2007148	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2245425	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2249346	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2762858	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2777908	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2777909	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2777917	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2794582	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2794583	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs474258	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs475233	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs475434	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs479094	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs480377	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs480498	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs486906	0.85[EUR][1000 genomes]
rs501300	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs505789	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs505837	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs507603	0.88[ASN][1000 genomes]
rs514421	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs518774	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs522534	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs530369	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs530854	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs538512	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs547776	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs549650	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs553830	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs555270	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs555526	0.89[ASN][1000 genomes]
rs589780	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs599185	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs600046	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs600553	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs605807	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs609521	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs612215	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs644412	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005808	chr1:179783922-179864710	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv1005051	chr1:179785643-179861950	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179795600-179834200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:179802400-179836200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr1:179803600-179833600	Weak transcription	Fetal Brain Male	brain
4	chr1:179807600-179827400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:179807800-179833800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr1:179808600-179837000	Strong transcription	Liver	Liver
7	chr1:179808600-179839800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr1:179808800-179836000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:179809800-179827800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr1:179810200-179828000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:179812200-179827800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:179812600-179842600	Weak transcription	Stomach Mucosa	stomach
13	chr1:179813200-179839200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:179813400-179834000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr1:179814200-179834400	Weak transcription	Fetal Heart	heart
16	chr1:179814400-179839200	Strong transcription	HSMM	muscle
17	chr1:179815000-179828400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr1:179815000-179839400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:179816000-179836000	Weak transcription	Colonic Mucosa	Colon
20	chr1:179816800-179826400	Weak transcription	Colon Smooth Muscle	Colon
21	chr1:179820200-179826200	Weak transcription	NHLF	lung
22	chr1:179820200-179829600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr1:179820200-179831600	Weak transcription	Esophagus	oesophagus
24	chr1:179820200-179834200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:179820400-179826200	Weak transcription	Rectal Smooth Muscle	rectum
26	chr1:179820400-179826200	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr1:179820400-179826400	Weak transcription	Thymus	Thymus
28	chr1:179820400-179829200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr1:179820400-179829800	Weak transcription	Psoas Muscle	Psoas
30	chr1:179820400-179831600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr1:179820400-179832200	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr1:179820400-179833600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr1:179820400-179834000	Weak transcription	Brain Cingulate Gyrus	brain
34	chr1:179820400-179841400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr1:179820400-179841800	Weak transcription	Small Intestine	intestine
36	chr1:179820400-179844200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr1:179820400-179845400	Weak transcription	Right Ventricle	heart
38	chr1:179820600-179831000	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr1:179820600-179832600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr1:179820600-179832800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr1:179820600-179834000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr1:179820600-179834000	Weak transcription	HSMMtube	muscle
43	chr1:179820800-179826400	Weak transcription	Fetal Thymus	thymus
44	chr1:179821000-179826400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr1:179821000-179826400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr1:179821000-179826400	Weak transcription	Brain Angular Gyrus	brain
47	chr1:179821000-179826400	Weak transcription	Brain Anterior Caudate	brain
48	chr1:179821000-179827800	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr1:179821000-179830200	Weak transcription	GM12878-XiMat	blood
50	chr1:179821000-179833400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links