Variant report

Variant	rs1573336
Chromosome Location	chr21:45240137-45240138
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:45238123..45243699-chr21:45249780..45254219,5	K562	blood:
2	chr21:45240125..45242679-chr21:45283332..45285060,2	MCF-7	breast:
3	chr21:45238343..45240639-chr21:45244780..45247104,2	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11700631	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11701439	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11701446	0.81[AFR][1000 genomes]
rs11701955	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11702496	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11702793	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11702828	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12483706	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13050364	0.81[EUR][1000 genomes]
rs13052408	0.94[CEU][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1573334	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1573335	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1573338	0.92[MEX][hapmap]
rs1573339	0.96[MEX][hapmap];0.83[TSI][hapmap]
rs1964982	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2070537	0.89[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2070539	0.86[CHB][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2186927	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2276246	0.94[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2838368	0.95[CEU][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2838370	0.87[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2838375	0.84[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs2838384	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2838393	0.94[CEU][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28648592	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35190140	0.83[ASN][1000 genomes]
rs35196921	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3819599	0.91[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4818867	0.83[ASN][1000 genomes]
rs57786602	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6518323	0.89[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7278524	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8132884	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs880987	0.86[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.84[MEX][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531545	chr21:45095397-45395904	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv913876	chr21:45119629-45267193	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	esv2830066	chr21:45133868-45258047	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv913880	chr21:45145286-45263920	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	nsv913881	chr21:45145286-45267193	Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv470904	chr21:45151045-45258047	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv913882	chr21:45151874-45370715	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
8	nsv834107	chr21:45155325-45294546	Enhancers Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
9	esv33817	chr21:45169412-46031810	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
10	nsv520305	chr21:45175958-45246326	Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
11	nsv834108	chr21:45178037-45369641	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
12	nsv913883	chr21:45191139-45252838	Weak transcription Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
13	nsv913884	chr21:45191139-45255836	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
14	nsv544469	chr21:45194085-45257959	Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
15	nsv913885	chr21:45206355-45249474	Weak transcription Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
16	nsv587718	chr21:45210932-45252838	Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
17	nsv1065007	chr21:45212880-45257959	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
18	nsv544470	chr21:45212880-45257959	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
19	nsv459292	chr21:45218440-45269841	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
20	nsv587719	chr21:45218440-45269841	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
21	nsv522204	chr21:45220483-45246326	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
22	nsv913886	chr21:45220483-45267193	Active TSS Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
23	esv1844567	chr21:45230974-45246326	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
24	nsv587720	chr21:45232322-45263920	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
25	esv19139	chr21:45232877-45241349	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
26	nsv516832	chr21:45237039-45240137	Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
27	nsv519385	chr21:45237039-45263920	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
28	esv2763257	chr21:45238052-45240137	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
29	esv1805861	chr21:45238052-45240140	ZNF genes & repeats Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
30	nsv442499	chr21:45238052-45240140	ZNF genes & repeats Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1573336	C21orf2	cis	parietal	SCAN
rs1573336	CSTB	Cis_1M	lymphoblastoid	RTeQTL
rs1573336	CSTB	cis	multi-tissue	Pritchard
rs1573336	LOC284837	cis	multi-tissue	Pritchard
rs1573336	LOC284837	cis	cerebellum	SCAN
rs1573336	CSTB	cis	lymphoblastoid	seeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45211000-45257200	Weak transcription	Right Atrium	heart
2	chr21:45232800-45241400	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr21:45232800-45244000	Weak transcription	Brain Angular Gyrus	brain
4	chr21:45234800-45245000	Weak transcription	Brain Anterior Caudate	brain
5	chr21:45235000-45244000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr21:45236000-45244200	Weak transcription	Right Ventricle	heart
7	chr21:45236000-45245000	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr21:45237000-45240600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr21:45238800-45240600	Weak transcription	Aorta	Aorta
10	chr21:45239600-45240600	Enhancers	Spleen	Spleen
11	chr21:45239800-45243600	Weak transcription	K562	blood
12	chr21:45240000-45244200	Weak transcription	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links