Variant report

Variant	rs10496028
Chromosome Location	chr2:54306454-54306455
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54303310..54306490-chr2:54307537..54312281,6	K562	blood:
2	chr2:54304842..54306570-chr2:54310702..54313482,3	K562	blood:

Variant related genes	Relation type
ENSG00000272156	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10183655	0.80[GIH][hapmap]
rs11676462	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11890838	0.88[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs11896815	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11898855	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs17039547	1.00[ASW][hapmap];0.95[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.84[JPT][hapmap];0.96[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17045452	0.81[CHD][hapmap];0.82[GIH][hapmap];0.84[JPT][hapmap];0.81[MEX][hapmap]
rs17045474	0.86[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17045488	0.86[CEU][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1877908	0.88[CHD][hapmap]
rs2287643	0.95[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2357896	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2909459	0.89[JPT][hapmap];1.00[YRI][hapmap]
rs34498089	0.89[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34773403	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3731967	0.81[CHD][hapmap];0.87[GIH][hapmap]
rs4671861	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55649409	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55705819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55930424	0.87[AFR][1000 genomes]
rs56193146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62137964	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62137976	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62137980	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62140990	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62141002	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6545381	0.85[AFR][1000 genomes]
rs6545386	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6713088	0.82[ASN][1000 genomes]
rs6714450	0.85[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs6721970	0.89[ASW][hapmap];0.91[CEU][hapmap];0.82[CHB][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.86[MKK][hapmap];0.86[TSI][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6751105	0.85[CHD][hapmap]
rs7559384	0.81[ASN][1000 genomes]
rs7565453	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7573551	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7576901	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7590819	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs805310	0.84[JPT][hapmap]
rs805316	0.88[LWK][hapmap];0.91[YRI][hapmap]
rs805338	1.00[YRI][hapmap]
rs805352	0.82[ASW][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap]
rs805365	0.82[ASW][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap]
rs805399	0.82[ASW][hapmap];0.87[GIH][hapmap]
rs805401	0.82[ASW][hapmap];0.82[GIH][hapmap]
rs805404	0.82[ASW][hapmap];0.86[GIH][hapmap]
rs805426	0.82[ASW][hapmap];0.95[GIH][hapmap]
rs805446	1.00[YRI][hapmap]
rs805449	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001246	chr2:54195654-54434832	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv1003205	chr2:54220049-54700843	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv2762639	chr2:54220049-54700855	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1002891	chr2:54227005-54682169	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv535722	chr2:54227005-54682169	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv1011690	chr2:54255361-54700843	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv431069	chr2:54260132-54434049	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv1010175	chr2:54292951-54343466	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	esv3425103	chr2:54305541-54309163	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10496028	MTIF2	cis	cerebellum	SCAN
rs10496028	PSME4	Cis_1M	lymphoblastoid	RTeQTL
rs10496028	PRDXDD1P	cis	parietal	SCAN
rs10496028	PSME4	cis	lymphoblastoid	seeQTL
rs10496028	PSME4	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54280800-54310000	Weak transcription	Ovary	ovary
2	chr2:54280800-54315000	Weak transcription	Adipose Nuclei	Adipose
3	chr2:54280800-54315200	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr2:54280800-54331000	Weak transcription	Aorta	Aorta
5	chr2:54281600-54308800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr2:54287000-54310000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr2:54287200-54307000	Weak transcription	Primary T cells from cord blood	blood
8	chr2:54289800-54317600	Weak transcription	Primary B cells from cord blood	blood
9	chr2:54291200-54342000	Weak transcription	Stomach Smooth Muscle	stomach
10	chr2:54292000-54308400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr2:54293400-54308400	Weak transcription	Fetal Muscle Leg	muscle
12	chr2:54293600-54310600	Weak transcription	HSMM	muscle
13	chr2:54294800-54315000	Weak transcription	Fetal Intestine Small	intestine
14	chr2:54295200-54312200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr2:54295400-54309800	Weak transcription	Fetal Brain Male	brain
16	chr2:54301600-54308200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:54302200-54308200	Weak transcription	HMEC	breast
18	chr2:54302200-54310600	Weak transcription	A549	lung
19	chr2:54302600-54308600	Weak transcription	NH-A	brain
20	chr2:54302600-54310400	Weak transcription	Osteobl	bone
21	chr2:54302800-54317800	Weak transcription	Left Ventricle	heart
22	chr2:54305000-54308000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr2:54305000-54315000	Weak transcription	Fetal Intestine Large	intestine
24	chr2:54305000-54315200	Weak transcription	Pancreas	Pancrea
25	chr2:54305400-54321600	Weak transcription	Lung	lung
26	chr2:54306000-54306600	Enhancers	Brain Hippocampus Middle	brain
27	chr2:54306200-54307400	Enhancers	Brain Anterior Caudate	brain
28	chr2:54306200-54307400	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr2:54306200-54307400	ZNF genes & repeats	K562	blood
30	chr2:54306400-54306600	Flanking Active TSS	Brain Cingulate Gyrus	brain
31	chr2:54306400-54306800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:54306400-54306800	Flanking Active TSS	Brain Substantia Nigra	brain
33	chr2:54306400-54307400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:54306400-54307800	Enhancers	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links