Variant report

Variant	rs8134733
Chromosome Location	chr21:40683459-40683460
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr21:40682578-40684658	K562	blood:	n/a	n/a
2	WRNIP1	chr21:40683422-40683489	GM12878	blood:	n/a	n/a
3	TBL1XR1	chr21:40683451-40683529	K562	blood:	n/a	n/a
4	POLR2A	chr21:40683070-40683484	K562	blood:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:40683319..40690926-chr21:40755872..40762716,23	MCF-7	breast:
2	chr21:40672762..40675001-chr21:40682440..40684098,2	K562	blood:
3	chr21:40682124..40685118-chr21:40763752..40765296,2	K562	blood:
4	chr21:40681596..40696529-chr21:40715399..40724266,46	K562	blood:
5	chr21:40645055..40648656-chr21:40680491..40684092,3	K562	blood:
6	chr21:40681416..40687854-chr21:40744378..40751195,8	K562	blood:
7	chr21:40554270..40557456-chr21:40682408..40685088,3	K562	blood:
8	chr21:40683271..40692626-chr21:40743960..40754349,22	MCF-7	breast:
9	chr21:40550424..40553042-chr21:40683249..40686279,3	K562	blood:
10	chr21:40682856..40693378-chr21:40754350..40765471,56	MCF-7	breast:
11	chr21:40591760..40593585-chr21:40682186..40684474,2	K562	blood:
12	chr21:40668014..40669940-chr21:40681557..40684495,2	K562	blood:
13	chr21:40553454..40557456-chr21:40682892..40687176,12	K562	blood:

No data

Variant related genes	Relation type
BRWD1-AS1	TF binding region
ENSG00000238556	Chromatin interaction
ENSG00000205581	Chromatin interaction
ENSG00000227406	Chromatin interaction
ENSG00000182093	Chromatin interaction
ENSG00000272991	Chromatin interaction
ENSG00000183527	Chromatin interaction
ENSG00000252915	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1041440	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10427502	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1065242	0.84[AMR][1000 genomes]
rs11910151	0.83[AMR][1000 genomes]
rs12151994	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12481860	0.82[AMR][1000 genomes]
rs12483216	0.82[AMR][1000 genomes]
rs12710453	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12710454	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13047663	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13047678	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13048178	0.86[AMR][1000 genomes]
rs13049280	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13339986	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13625	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1541102	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1984022	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2026265	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2026267	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2150415	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2234543	0.86[AMR][1000 genomes]
rs2735306	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2735309	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2776307	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2776308	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2776309	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs28360661	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836925	0.82[AMR][1000 genomes]
rs2836927	0.82[AMR][1000 genomes]
rs2836929	0.80[AMR][1000 genomes]
rs2836933	0.83[AMR][1000 genomes]
rs2836938	0.88[AMR][1000 genomes]
rs2836944	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836953	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2836955	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836957	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836964	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836965	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836967	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836968	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836972	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836973	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2836974	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2836977	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2989330	0.80[EUR][1000 genomes]
rs34035316	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34294410	0.82[AMR][1000 genomes]
rs34433511	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34478864	0.80[AMR][1000 genomes]
rs34578707	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34672724	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34978594	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35068861	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35123057	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35386515	0.80[AMR][1000 genomes]
rs35560196	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35571600	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35774464	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36113648	0.81[AMR][1000 genomes]
rs55836299	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56306759	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6517519	0.82[AMR][1000 genomes]
rs6517523	0.84[AMR][1000 genomes]
rs6517526	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6517527	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6517533	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6517538	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66465538	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68004583	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68090597	0.82[AMR][1000 genomes]
rs7277978	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7282624	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7283420	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7283516	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7283569	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73221193	0.84[AMR][1000 genomes]
rs7354783	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8127087	0.80[AMR][1000 genomes]
rs8128026	0.83[AMR][1000 genomes]
rs8128102	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8128620	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8128734	0.86[AMR][1000 genomes]
rs8128827	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8128894	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8129147	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8129303	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8129355	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8129416	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8130984	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8131965	0.87[AMR][1000 genomes]
rs8133146	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9941894	0.84[AMR][1000 genomes];0.92[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	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
2	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
3	esv3429298	chr21:40670131-40688774	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv913744	chr21:40670167-40757973	Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs8134733	HMGN1	Cis_1M	lymphoblastoid	RTeQTL
rs8134733	PSMG1	cis	Skin Sun Exposed Lower leg	GTEx
rs8134733	PSMG1	cis	lung	GTEx
rs8134733	PSMG1	cis	Muscle Skeletal	GTEx
rs8134733	PSMG1	cis	Esophagus Mucosa	GTEx
rs8134733	PSMG1	cis	Artery Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40641400-40683800	Strong transcription	Placenta	Placenta
2	chr21:40643800-40684200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr21:40656400-40683800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr21:40664000-40684200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr21:40665000-40683800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr21:40665200-40684400	Weak transcription	Colonic Mucosa	Colon
7	chr21:40667000-40684000	Weak transcription	HSMMtube	muscle
8	chr21:40667000-40684200	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr21:40669200-40684200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr21:40669400-40684000	Weak transcription	HUVEC	blood vessel
11	chr21:40669400-40684400	Weak transcription	Esophagus	oesophagus
12	chr21:40669800-40683800	Weak transcription	Brain Substantia Nigra	brain
13	chr21:40670400-40683800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr21:40672200-40684000	Weak transcription	Aorta	Aorta
15	chr21:40672400-40684000	Weak transcription	Small Intestine	intestine
16	chr21:40672600-40683800	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr21:40672600-40684400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr21:40672800-40683800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr21:40673600-40683600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr21:40673600-40683600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr21:40673600-40683600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr21:40673600-40683800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr21:40673600-40684000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr21:40673600-40684400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr21:40673600-40684600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr21:40673800-40683800	Weak transcription	Fetal Kidney	kidney
27	chr21:40675000-40683800	Weak transcription	A549	lung
28	chr21:40675800-40683800	Weak transcription	Brain Cingulate Gyrus	brain
29	chr21:40675800-40684200	Weak transcription	Pancreas	Pancrea
30	chr21:40675800-40684400	Weak transcription	Gastric	stomach
31	chr21:40675800-40684400	Weak transcription	Spleen	Spleen
32	chr21:40676400-40683600	Weak transcription	Colon Smooth Muscle	Colon
33	chr21:40676600-40683800	Weak transcription	Stomach Smooth Muscle	stomach
34	chr21:40676600-40684000	Weak transcription	Brain Germinal Matrix	brain
35	chr21:40676800-40683600	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr21:40676800-40683800	Weak transcription	GM12878-XiMat	blood
37	chr21:40677200-40683800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr21:40678200-40683800	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr21:40679400-40683600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr21:40679400-40683800	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr21:40679400-40683800	Strong transcription	Primary B cells from peripheral blood	blood
42	chr21:40679600-40683800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
43	chr21:40679800-40683600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr21:40679800-40683800	Strong transcription	Fetal Lung	lung
45	chr21:40680000-40683600	Strong transcription	Fetal Muscle Leg	muscle
46	chr21:40680200-40683600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr21:40680200-40683800	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr21:40680400-40684000	Weak transcription	Right Ventricle	heart
49	chr21:40680600-40683800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr21:40680800-40683600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links