Variant report

Variant	rs2298018
Chromosome Location	chr1:45813441-45813442
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45769536..45771577-chr1:45812790..45815177,2	K562	blood:
2	chr1:45478794..45481756-chr1:45811013..45814397,3	K562	blood:
3	chr1:45769560..45771577-chr1:45812920..45815177,2	K562	blood:
4	chr1:45811184..45813641-chr1:45972187..45974707,2	K562	blood:
5	chr1:45812595..45814836-chr1:46042720..46044656,2	K562	blood:
6	chr1:45293740..45296221-chr1:45811017..45813846,2	K562	blood:
7	chr1:45810406..45813503-chr1:45959640..45961736,3	K562	blood:
8	chr1:45478234..45481000-chr1:45809377..45813854,5	K562	blood:
9	chr1:45810813..45813793-chr1:45880439..45883118,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000126088	Chromatin interaction
ENSG00000236872	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs1006216	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs1007858	0.81[EUR][1000 genomes]
rs10789465	0.83[CHB][hapmap]
rs1084166	0.82[EUR][1000 genomes]
rs10890327	0.85[EUR][1000 genomes]
rs10890330	0.86[CEU][hapmap]
rs11211101	1.00[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11211108	0.86[EUR][1000 genomes]
rs11211111	0.91[CEU][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.81[EUR][1000 genomes]
rs11211117	0.82[EUR][1000 genomes]
rs11211118	0.82[EUR][1000 genomes]
rs12037201	0.83[EUR][1000 genomes]
rs12037411	0.91[EUR][1000 genomes]
rs12046816	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs12097497	0.85[EUR][1000 genomes]
rs12139364	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs12410493	0.83[EUR][1000 genomes]
rs12738318	0.83[CHB][hapmap]
rs12743512	0.83[CHB][hapmap]
rs1417578	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1494812	0.89[CEU][hapmap];0.83[CHB][hapmap];0.85[EUR][1000 genomes]
rs1538969	0.81[EUR][1000 genomes]
rs1538970	0.83[EUR][1000 genomes]
rs17395553	0.91[EUR][1000 genomes]
rs1771551	0.88[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1826691	0.91[CEU][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];0.85[EUR][1000 genomes]
rs2050884	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2055145	0.86[CEU][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap]
rs2088100	0.85[EUR][1000 genomes]
rs2153607	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2153608	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2153609	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2185549	1.00[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2275276	0.83[CHB][hapmap]
rs2487442	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];0.90[TSI][hapmap];0.93[YRI][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2492836	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2492840	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28555082	0.82[EUR][1000 genomes]
rs3219463	1.00[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3219472	1.00[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3219489	1.00[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3790582	0.91[CEU][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.85[EUR][1000 genomes]
rs4520450	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs4660301	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4660849	1.00[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4660851	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4660852	1.00[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4660853	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4660854	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4660855	0.83[EUR][1000 genomes]
rs4660858	0.91[CEU][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.82[EUR][1000 genomes]
rs61788261	0.84[EUR][1000 genomes]
rs61788281	0.82[EUR][1000 genomes]
rs61791362	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61791368	0.83[EUR][1000 genomes]
rs61791369	0.86[EUR][1000 genomes]
rs6657284	0.91[CEU][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap]
rs72686460	0.81[EUR][1000 genomes]
rs7417107	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7525849	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7528573	0.82[EUR][1000 genomes]
rs7531253	0.91[CEU][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.86[EUR][1000 genomes]
rs7532762	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7536135	0.85[EUR][1000 genomes]
rs7543428	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7544178	1.00[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7553318	1.00[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs781058	0.83[CHB][hapmap]
rs781226	0.94[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.93[YRI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs781230	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs781232	0.89[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs884962	0.95[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9326141	1.00[CEU][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs937291	0.83[CHB][hapmap]
rs9429072	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9429073	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9429074	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9429076	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9429158	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9429159	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9429160	1.00[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9429161	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[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	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1014509	chr1:45687523-45887501	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv997548	chr1:45733596-45955845	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv534942	chr1:45733596-45955845	Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv482356	chr1:45750459-45915545	Enhancers Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
6	esv2750837	chr1:45796115-45908263	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2298018	SPATA19	trans	parietal	SCAN
rs2298018	TESK2	cis	Whole Blood	GTEx
rs2298018	IPP	cis	lymphoblastoid	seeQTL
rs2298018	ST3GAL3	cis	parietal	SCAN
rs2298018	MAST2	cis	cerebellum	SCAN
rs2298018	MUTYH	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45806600-45821600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:45807200-45814200	Weak transcription	Fetal Brain Male	brain
3	chr1:45807200-45825800	Weak transcription	Small Intestine	intestine
4	chr1:45807400-45813600	Weak transcription	NHDF-Ad	bronchial
5	chr1:45807800-45813600	Strong transcription	Fetal Intestine Large	intestine
6	chr1:45807800-45813600	Strong transcription	Fetal Intestine Small	intestine
7	chr1:45807800-45813800	Strong transcription	Fetal Stomach	stomach
8	chr1:45808200-45814000	Weak transcription	Stomach Mucosa	stomach
9	chr1:45808400-45813600	Weak transcription	Fetal Heart	heart
10	chr1:45808800-45813800	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr1:45808800-45825600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr1:45809200-45815000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr1:45810000-45819800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr1:45810200-45813600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:45810200-45813600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr1:45810600-45813600	Weak transcription	Left Ventricle	heart
17	chr1:45810600-45813800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr1:45810600-45814000	Weak transcription	Pancreas	Pancrea
19	chr1:45810600-45814600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr1:45810600-45825600	Weak transcription	Fetal Kidney	kidney
21	chr1:45810800-45813600	Weak transcription	Colon Smooth Muscle	Colon
22	chr1:45810800-45813600	Weak transcription	NHLF	lung
23	chr1:45810800-45820800	Weak transcription	HUVEC	blood vessel
24	chr1:45811000-45813600	Weak transcription	HSMM	muscle
25	chr1:45811000-45813600	Weak transcription	NH-A	brain
26	chr1:45811000-45813800	Weak transcription	Osteobl	bone
27	chr1:45811000-45814000	Weak transcription	Aorta	Aorta
28	chr1:45811000-45814200	Weak transcription	Adipose Nuclei	Adipose
29	chr1:45811200-45813600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr1:45811200-45813600	Weak transcription	Esophagus	oesophagus
31	chr1:45811200-45813600	Weak transcription	Ovary	ovary
32	chr1:45811200-45813800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr1:45811200-45814000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:45811200-45814000	Weak transcription	Brain Germinal Matrix	brain
35	chr1:45811200-45820800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr1:45811200-45825600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr1:45811200-45825600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr1:45811200-45825600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr1:45811400-45817000	Weak transcription	HepG2	liver
40	chr1:45811400-45825800	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr1:45811400-45825800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr1:45811600-45813600	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr1:45811600-45813600	Weak transcription	A549	lung
44	chr1:45811600-45825800	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr1:45811800-45813600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr1:45811800-45814600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr1:45812000-45815200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr1:45812000-45826000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr1:45812200-45814000	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr1:45812200-45817200	Weak transcription	Sigmoid Colon	Sigmoid Colon

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