Variant report

Variant	rs2281486
Chromosome Location	chr1:173822221-173822222
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:173807218..173809787-chr1:173821363..173824088,2	MCF-7	breast:
2	chr1:173761583..173764570-chr1:173821464..173823065,2	K562	blood:

Extended variants
information (count: 88 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10489894	1.00[YRI][hapmap]
rs10912670	0.85[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs10912671	0.95[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.88[ASN][1000 genomes]
rs12082131	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs12086229	0.90[ASN][1000 genomes]
rs12561931	0.95[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12564699	0.90[ASN][1000 genomes]
rs12565915	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12566945	0.90[ASN][1000 genomes]
rs1322774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846439	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16846529	0.90[LWK][hapmap];0.91[YRI][hapmap]
rs1951625	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2067079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2144708	0.95[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.93[ASN][1000 genomes]
rs2208850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2227588	0.85[CHB][hapmap]
rs2227612	0.85[CHB][hapmap]
rs2273366	0.95[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2295366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28804123	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35571466	1.00[YRI][hapmap]
rs3791020	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[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];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs45467799	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4558043	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4652283	0.85[CHB][hapmap]
rs4652298	0.85[CHB][hapmap]
rs4652328	0.85[CHB][hapmap]
rs55633896	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55829688	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56019876	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56048122	0.94[ASN][1000 genomes]
rs56138893	0.85[ASN][1000 genomes]
rs56369162	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56928371	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57799150	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs58287165	0.85[ASN][1000 genomes]
rs58825445	0.87[ASN][1000 genomes]
rs59858609	0.85[ASN][1000 genomes]
rs60264384	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61826805	0.85[ASN][1000 genomes]
rs61826806	0.85[ASN][1000 genomes]
rs61826809	0.85[ASN][1000 genomes]
rs61826810	0.85[ASN][1000 genomes]
rs61826812	0.88[ASN][1000 genomes]
rs61826813	0.88[ASN][1000 genomes]
rs61826821	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61826856	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61826857	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61827860	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61827861	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61827863	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61827865	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs61827867	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61827870	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61827876	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61827877	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61827881	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61827925	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6413827	0.95[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.88[ASN][1000 genomes]
rs6425253	0.81[ASN][1000 genomes]
rs6425258	0.95[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6425261	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6668702	0.90[ASN][1000 genomes]
rs6673175	0.90[ASN][1000 genomes]
rs6674381	0.92[ASN][1000 genomes]
rs6681766	0.85[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs6691001	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6696680	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs6698314	0.90[LWK][hapmap];1.00[YRI][hapmap]
rs7514556	0.95[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs7515721	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs7521884	0.94[ASN][1000 genomes]
rs7525115	0.90[LWK][hapmap];1.00[YRI][hapmap]
rs7530546	0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7546048	0.93[ASN][1000 genomes]
rs7548171	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7552741	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs9425416	0.93[ASN][1000 genomes]
rs9425431	0.85[CHB][hapmap]
rs9425433	0.85[CHB][hapmap]
rs9425745	0.95[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.85[TSI][hapmap];0.93[ASN][1000 genomes]
rs9425756	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9660881	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][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	nsv1012384	chr1:173614816-173974426	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
2	nsv831926	chr1:173702403-173894667	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	291 gene(s)	inside rSNPs	diseases
3	esv2757761	chr1:173810642-173955943	Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
4	esv2758978	chr1:173810642-173955943	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2281486	PRDX6	cis	parietal	SCAN
rs2281486	SLC9A11	cis	parietal	SCAN
rs2281486	DARS2	cis	cerebellum	SCAN
rs2281486	RABGAP1L	cis	parietal	SCAN
rs2281486	TNN	cis	parietal	SCAN
rs2281486	DARS2	cis	Muscle Skeletal	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:173794400-173832800	Weak transcription	Fetal Heart	heart
2	chr1:173794600-173832000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr1:173794600-173832000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:173794600-173832600	Weak transcription	Brain Substantia Nigra	brain
5	chr1:173794600-173833800	Weak transcription	Stomach Mucosa	stomach
6	chr1:173794800-173834000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:173795000-173826200	Weak transcription	Psoas Muscle	Psoas
8	chr1:173795000-173834600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:173795200-173822400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr1:173795200-173824600	Weak transcription	Gastric	stomach
11	chr1:173797200-173828400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:173799600-173828800	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr1:173801200-173825000	Weak transcription	Brain Angular Gyrus	brain
14	chr1:173803000-173826600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr1:173806800-173822800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr1:173809200-173825200	Weak transcription	NHDF-Ad	bronchial
17	chr1:173809800-173831800	Weak transcription	Colonic Mucosa	Colon
18	chr1:173811000-173824600	Weak transcription	Colon Smooth Muscle	Colon
19	chr1:173811000-173825000	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr1:173811200-173825000	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr1:173811200-173829200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr1:173813200-173823000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr1:173813200-173824800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr1:173813200-173831800	Weak transcription	Right Ventricle	heart
25	chr1:173813200-173832000	Weak transcription	Small Intestine	intestine
26	chr1:173813400-173831000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr1:173813600-173825400	Weak transcription	Brain Anterior Caudate	brain
28	chr1:173814600-173826400	Weak transcription	Hela-S3	cervix
29	chr1:173815000-173826000	Weak transcription	Esophagus	oesophagus
30	chr1:173815600-173822400	Weak transcription	Fetal Brain Female	brain
31	chr1:173816000-173822400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr1:173816000-173825000	Weak transcription	Spleen	Spleen
33	chr1:173817200-173823400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr1:173817800-173822600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr1:173818200-173831600	Weak transcription	Fetal Brain Male	brain
36	chr1:173818400-173829000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr1:173818400-173829800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr1:173818600-173824200	Strong transcription	Primary hematopoietic stem cells	blood
39	chr1:173818600-173825200	Strong transcription	Fetal Stomach	stomach
40	chr1:173818600-173829600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr1:173818600-173830200	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr1:173818600-173834800	Strong transcription	Fetal Muscle Leg	muscle
43	chr1:173818600-173834800	Strong transcription	Monocytes-CD14+_RO01746	blood
44	chr1:173818800-173822400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr1:173818800-173827200	Strong transcription	Primary T cells from cord blood	blood
46	chr1:173818800-173827800	Strong transcription	Dnd41	blood
47	chr1:173819000-173824200	Strong transcription	GM12878-XiMat	blood
48	chr1:173819200-173828200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr1:173819200-173833200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr1:173819200-173833800	Strong transcription	Primary T helper cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links