Variant report

Variant	rs2150413
Chromosome Location	chr21:40614878-40614879
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:40604603..40606220-chr21:40613422..40615728,2	K562	blood:
2	21:40614587-40619915..21:40757151-40764378	K562	blood:

Variant related genes	Relation type
ENSG00000182093	Chromatin interaction

Extended variants
information (count: 122 )
Associated
traits (count: 22 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs1029004	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10854396	0.82[ASN][1000 genomes]
rs11088466	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11088470	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11088471	0.87[YRI][hapmap]
rs11700813	0.81[EUR][1000 genomes]
rs11701805	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11702505	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11910232	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11911087	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12482181	0.85[ASW][hapmap];0.89[YRI][hapmap]
rs12483559	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12627205	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13047518	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13049907	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13625	0.85[ASW][hapmap];0.89[YRI][hapmap]
rs14194	0.85[ASW][hapmap];0.89[YRI][hapmap]
rs1541102	0.85[ASW][hapmap];0.89[YRI][hapmap]
rs1888488	0.92[ASW][hapmap];0.96[YRI][hapmap]
rs1980407	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1984022	0.89[YRI][hapmap]
rs2026265	0.89[YRI][hapmap]
rs2037925	0.92[ASW][hapmap]
rs2056844	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2070865	0.92[CEU][hapmap];0.86[CHB][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap]
rs2142111	0.89[YRI][hapmap]
rs2150411	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2150414	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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2150415	0.85[ASW][hapmap];0.87[YRI][hapmap]
rs2183573	0.86[ASW][hapmap]
rs2234543	0.85[ASW][hapmap];0.89[YRI][hapmap]
rs2245455	0.92[ASW][hapmap];0.92[YRI][hapmap]
rs2297256	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2410123	0.92[ASW][hapmap];0.85[YRI][hapmap]
rs2836922	0.81[EUR][1000 genomes]
rs2836925	0.85[ASW][hapmap];0.89[YRI][hapmap]
rs2836926	1.00[CEU][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2836929	0.85[ASW][hapmap];0.89[YRI][hapmap]
rs2836930	1.00[CEU][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2836931	1.00[CEU][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2836932	0.85[ASW][hapmap];0.89[YRI][hapmap]
rs2836933	0.89[YRI][hapmap]
rs2836934	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2836940	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2836942	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2836943	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2836945	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836948	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836949	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2836952	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2836956	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836957	0.89[YRI][hapmap]
rs2836958	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836959	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836964	0.85[ASW][hapmap];0.89[YRI][hapmap]
rs2836965	0.85[ASW][hapmap];0.89[YRI][hapmap]
rs2836966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2836967	0.89[YRI][hapmap]
rs2836968	0.85[ASW][hapmap];0.89[YRI][hapmap]
rs2836974	0.85[ASW][hapmap];0.89[YRI][hapmap]
rs2836975	0.86[ASW][hapmap]
rs2836980	0.80[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2836981	0.92[ASW][hapmap];0.89[YRI][hapmap]
rs2836982	0.92[ASW][hapmap];0.89[YRI][hapmap]
rs2836983	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2836984	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2836985	1.00[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2836986	0.85[YRI][hapmap]
rs2836987	0.92[ASW][hapmap];0.85[YRI][hapmap]
rs2836988	0.92[ASW][hapmap]
rs3171465	1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34705151	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35769610	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35994303	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs418298	0.86[ASW][hapmap]
rs418359	0.86[ASW][hapmap]
rs419469	0.92[ASW][hapmap]
rs428602	1.00[YRI][hapmap]
rs4624474	0.92[ASW][hapmap];0.96[YRI][hapmap]
rs4816617	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4816618	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4818001	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4818015	0.86[ASW][hapmap]
rs4818018	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4818019	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59916147	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62223011	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62223039	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62223052	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6517519	0.85[ASW][hapmap];0.89[YRI][hapmap]
rs6517523	0.85[ASW][hapmap];0.89[YRI][hapmap]
rs6517526	0.85[ASW][hapmap];0.89[YRI][hapmap]
rs6517538	0.85[ASW][hapmap];0.89[YRI][hapmap]
rs7276046	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7278297	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7279497	1.00[CEU][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7280375	0.85[ASW][hapmap];0.89[YRI][hapmap]
rs7281853	0.92[ASW][hapmap];0.89[YRI][hapmap]
rs7282582	0.85[ASW][hapmap];0.88[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.80[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.90[AMR][1000 genomes]
rs7282604	0.86[ASW][hapmap]
rs7283516	0.82[YRI][hapmap]
rs8127087	0.89[YRI][hapmap]
rs8127379	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8128026	0.87[YRI][hapmap]
rs8128102	0.85[YRI][hapmap]
rs8129595	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8130162	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8130240	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8130320	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8130984	0.92[YRI][hapmap]
rs8131132	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8132143	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8132285	0.89[YRI][hapmap]
rs8132424	0.80[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8133928	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8134214	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8134843	0.90[EUR][1000 genomes]
rs9981301	0.96[YRI][hapmap]

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	nsv1056683	chr21:40570023-40673210	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv459259	chr21:40571246-40701169	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv587480	chr21:40571246-40701169	Strong transcription Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv587481	chr21:40598721-40627020	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:22)

SNP	Gene	Cis/trans	Tissue	Source
rs2150413	HMGN1	cis	brain	seeQTL
rs2150413	HMGN1	trans	brain	seeQTL
rs2150413	PSMG1	cis	Skin Sun Exposed Lower leg	GTEx
rs2150413	PSMG1	cis	parietal	SCAN
rs2150413	LOC643790	trans	multi-tissue	Pritchard
rs2150413	BRWD1	cis	lymphoblastoid	seeQTL
rs2150413	PSMG1	cis	Esophagus Mucosa	GTEx
rs2150413	PSMG1	cis	lung	GTEx
rs2150413	WRB	cis	multi-tissue	Pritchard
rs2150413	BRWD1	cis	parietal	SCAN
rs2150413	PSMG1	cis	Artery Tibial	GTEx
rs2150413	DSCR2	cis	multi-tissue	Pritchard
rs2150413	HMGN1	cis	lymphoblastoid	seeQTL
rs2150413	BRWD1	cis	Cerebellum	GTEx
rs2150413	BRWD1	cis	cerebellum	SCAN
rs2150413	BRWD1	cis	Lymphoblastoid	GTEx
rs2150413	BRWD1	cis	Frontal Cortex	GTEx
rs2150413	BRWD1	cis	Temporal Cortex	GTEx
rs2150413	BRWD1	cis	Brain Pons	GTEx
rs2150413	C21orf107	cis	multi-tissue	Pritchard
rs2150413	BRWD1	cis	multi-tissue	Pritchard
rs2150413	HMGN1	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40563000-40640600	Strong transcription	Placenta	Placenta
2	chr21:40563000-40643600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr21:40563400-40653400	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr21:40563400-40660000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr21:40563600-40653600	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr21:40565000-40654600	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr21:40565200-40653600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr21:40565400-40653600	Strong transcription	Dnd41	blood
9	chr21:40565600-40615000	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr21:40566000-40653600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr21:40572000-40636800	Weak transcription	Psoas Muscle	Psoas
12	chr21:40573800-40631000	Weak transcription	Small Intestine	intestine
13	chr21:40581400-40635400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr21:40582600-40622000	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr21:40582800-40654000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr21:40591200-40621600	Strong transcription	Duodenum Mucosa	Duodenum
17	chr21:40591200-40622200	Strong transcription	Liver	Liver
18	chr21:40591400-40625200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr21:40592000-40622400	Strong transcription	K562	blood
20	chr21:40593400-40650800	Strong transcription	Primary T helper cells fromperipheralblood	blood
21	chr21:40595800-40624000	Strong transcription	Primary B cells from peripheral blood	blood
22	chr21:40597200-40635600	Weak transcription	Fetal Heart	heart
23	chr21:40598200-40629800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr21:40598600-40625000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr21:40599200-40623800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr21:40603000-40627800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr21:40603200-40653400	Weak transcription	Right Atrium	heart
28	chr21:40608000-40616600	Weak transcription	Fetal Kidney	kidney
29	chr21:40608400-40616400	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr21:40608400-40616600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr21:40608400-40617800	Weak transcription	A549	lung
32	chr21:40608400-40628400	Weak transcription	Lung	lung
33	chr21:40608400-40632200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr21:40608400-40632600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr21:40608400-40634200	Weak transcription	NHLF	lung
36	chr21:40608400-40638200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr21:40608400-40667200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr21:40608600-40617000	Weak transcription	Colonic Mucosa	Colon
39	chr21:40608600-40617000	Weak transcription	Fetal Intestine Small	intestine
40	chr21:40608600-40617000	Weak transcription	Pancreas	Pancrea
41	chr21:40608600-40618600	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr21:40608600-40618800	Weak transcription	Ovary	ovary
43	chr21:40608600-40627000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr21:40608600-40628400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr21:40608600-40636400	Weak transcription	Aorta	Aorta
46	chr21:40608800-40617000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr21:40608800-40617200	Weak transcription	Stomach Mucosa	stomach
48	chr21:40608800-40618600	Weak transcription	Gastric	stomach
49	chr21:40608800-40620200	Weak transcription	Spleen	Spleen
50	chr21:40608800-40623600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links