Variant report

Variant	rs2836949
Chromosome Location	chr21:40602456-40602457
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr21:40602436-40602497	GM12878	blood:	n/a	n/a
2	POLR2A	chr21:40602065-40603036	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:40602448..40605045-chr21:40605736..40607319,2	K562	blood:
2	chr21:40589600..40591908-chr21:40602305..40604047,2	K562	blood:
3	chr21:40602289..40604074-chr21:40606998..40609550,3	MCF-7	breast:

Variant related genes	Relation type
BRWD1	TF binding region
ENSG00000237373	Chromatin interaction
ENSG00000229623	Chromatin interaction
ENSG00000185658	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1029004	0.84[AFR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11088466	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11088470	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11701805	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11702505	0.81[EUR][1000 genomes]
rs11910232	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11911087	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12483559	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12627205	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13047518	0.80[EUR][1000 genomes]
rs13049907	0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1980407	0.88[EUR][1000 genomes]
rs2056844	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap];0.97[YRI][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2070865	0.96[CEU][hapmap];0.85[JPT][hapmap]
rs2150411	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes]
rs2150413	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2150414	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2297256	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.89[EUR][1000 genomes]
rs2836926	0.96[CEU][hapmap];0.95[JPT][hapmap];0.97[YRI][hapmap];0.88[EUR][1000 genomes]
rs2836930	0.96[CEU][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes]
rs2836931	0.96[CEU][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes]
rs2836934	0.96[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap];0.90[EUR][1000 genomes]
rs2836940	0.97[YRI][hapmap];0.84[AFR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2836942	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap];0.97[YRI][hapmap];0.84[AFR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2836943	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.97[YRI][hapmap];0.82[AFR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2836945	0.96[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836948	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap];0.97[YRI][hapmap];0.90[AFR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2836952	0.96[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2836956	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2836958	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2836959	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2836966	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2836980	0.96[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes]
rs2836983	0.96[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2836984	0.81[EUR][1000 genomes]
rs2836985	0.96[CEU][hapmap];0.85[JPT][hapmap];0.81[EUR][1000 genomes]
rs3171465	0.96[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[EUR][1000 genomes]
rs34705151	0.87[EUR][1000 genomes]
rs35769610	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35994303	0.85[EUR][1000 genomes]
rs4816617	0.88[EUR][1000 genomes]
rs4816618	0.90[AFR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4818001	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes]
rs4818018	0.85[EUR][1000 genomes]
rs4818019	0.86[EUR][1000 genomes]
rs59916147	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62223011	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62223039	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62223052	0.81[EUR][1000 genomes]
rs7276046	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7278297	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7279497	0.96[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs7282582	0.92[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap]
rs8127379	0.93[AFR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8129595	0.86[EUR][1000 genomes]
rs8130162	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8130240	0.88[EUR][1000 genomes]
rs8130320	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8131132	0.88[EUR][1000 genomes]
rs8132143	1.00[CEU][hapmap];0.92[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8132424	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8133928	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8134214	0.88[EUR][1000 genomes]
rs8134843	0.88[EUR][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	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2836949	PSMG1	cis	lung	GTEx
rs2836949	HMGN1	cis	multi-tissue	Pritchard
rs2836949	PSMG1	cis	Skin Sun Exposed Lower leg	GTEx
rs2836949	PSMG1	cis	Artery Tibial	GTEx
rs2836949	HMGN1	Cis_1M	lymphoblastoid	RTeQTL
rs2836949	BRWD1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40556200-40602600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr21:40563000-40640600	Strong transcription	Placenta	Placenta
3	chr21:40563000-40643600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr21:40563400-40653400	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr21:40563400-40660000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr21:40563600-40653600	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr21:40564600-40612600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr21:40565000-40654600	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr21:40565200-40653600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr21:40565400-40604200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr21:40565400-40612600	Strong transcription	Primary monocytes fromperipheralblood	blood
12	chr21:40565400-40653600	Strong transcription	Dnd41	blood
13	chr21:40565600-40615000	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr21:40566000-40653600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr21:40566400-40613200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr21:40569800-40607800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr21:40572000-40636800	Weak transcription	Psoas Muscle	Psoas
18	chr21:40573800-40631000	Weak transcription	Small Intestine	intestine
19	chr21:40578000-40607600	Weak transcription	Aorta	Aorta
20	chr21:40578600-40608000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr21:40578800-40606600	Weak transcription	Brain Substantia Nigra	brain
22	chr21:40580400-40606400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr21:40580600-40607600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr21:40580800-40607200	Weak transcription	Spleen	Spleen
25	chr21:40581400-40635400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr21:40581800-40607200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr21:40582200-40614200	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr21:40582600-40622000	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr21:40582800-40654000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr21:40583600-40606800	Weak transcription	NHLF	lung
31	chr21:40588800-40607800	Weak transcription	Right Ventricle	heart
32	chr21:40590000-40605600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr21:40590200-40607200	Weak transcription	NHEK	skin
34	chr21:40590200-40607600	Weak transcription	Brain Hippocampus Middle	brain
35	chr21:40590200-40608000	Weak transcription	Stomach Mucosa	stomach
36	chr21:40590400-40604600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr21:40590600-40607400	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr21:40591200-40621600	Strong transcription	Duodenum Mucosa	Duodenum
39	chr21:40591200-40622200	Strong transcription	Liver	Liver
40	chr21:40591400-40625200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr21:40592000-40622400	Strong transcription	K562	blood
42	chr21:40593400-40604800	Strong transcription	Fetal Intestine Large	intestine
43	chr21:40593400-40607200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr21:40593400-40613400	Strong transcription	Fetal Thymus	thymus
45	chr21:40593400-40650800	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr21:40593600-40613200	Strong transcription	Primary T cells from cord blood	blood
47	chr21:40594200-40612200	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr21:40594400-40606600	Weak transcription	A549	lung
49	chr21:40594400-40607800	Weak transcription	Rectal Smooth Muscle	rectum
50	chr21:40595600-40606000	Weak transcription	HMEC	breast

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