Variant report

Variant	rs2838412
Chromosome Location	chr21:45249506-45249507
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:45230338..45231005-chr21:45249127..45250028,2	MCF-7	breast:
2	chr21:45249294..45252686-chr21:45284746..45287890,3	K562	blood:
3	chr21:45248431..45251491-chr21:45282831..45285581,3	MCF-7	breast:
4	chr21:45242806..45245083-chr21:45249324..45252265,2	MCF-7	breast:
5	chr21:45248939..45255746-chr21:45272255..45276727,7	K562	blood:
6	chr21:45231798..45234751-chr21:45247944..45249688,2	K562	blood:
7	chr21:45249286..45250425-chr21:45358859..45359776,4	MCF-7	breast:
8	chr21:45249455..45252079-chr21:45279419..45281351,2	K562	blood:
9	chr21:45248952..45249750-chr21:45395021..45396037,3	MCF-7	breast:
10	chr21:45249077..45249616-chr21:45337283..45338226,2	K562	blood:
11	chr21:45248181..45251000-chr21:45264176..45267243,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000215458	Chromatin interaction
ENSG00000226543	Chromatin interaction
ENSG00000160216	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs13050410	1.00[ASN][1000 genomes]
rs13052800	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17174789	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838403	0.81[ASW][hapmap];0.82[CEU][hapmap];0.86[MEX][hapmap];1.00[YRI][hapmap]
rs2838408	0.82[CEU][hapmap]
rs2838411	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838413	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34385375	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34746583	0.84[AMR][1000 genomes]
rs4290737	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4419312	0.81[EUR][1000 genomes]
rs4524200	0.81[EUR][1000 genomes]
rs4819319	1.00[ASN][1000 genomes]
rs57729293	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60094038	1.00[ASN][1000 genomes]
rs7277069	1.00[ASN][1000 genomes]
rs73224989	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73224990	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73906653	1.00[ASN][1000 genomes]
rs753125	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 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	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2838412	CBS	cis	parietal	SCAN
rs2838412	CSTB	cis	lymphoblastoid	seeQTL
rs2838412	MX1	cis	cerebellum	SCAN
rs2838412	PABPC5	trans	parietal	SCAN
rs2838412	C21orf2	cis	cerebellum	SCAN
rs2838412	C21orf33	cis	cerebellum	SCAN
rs2838412	RRP1B	cis	cerebellum	SCAN
rs2838412	KRTAP10-12	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45211000-45257200	Weak transcription	Right Atrium	heart
2	chr21:45246600-45250200	Weak transcription	Spleen	Spleen
3	chr21:45246800-45250400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr21:45246800-45251200	Weak transcription	Right Ventricle	heart
5	chr21:45247000-45249800	Weak transcription	Gastric	stomach
6	chr21:45247000-45255600	Weak transcription	Esophagus	oesophagus
7	chr21:45247200-45249600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr21:45247200-45249600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr21:45248400-45250000	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr21:45248400-45250000	Enhancers	Monocytes-CD14+_RO01746	blood
11	chr21:45249200-45249800	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr21:45249200-45250000	Flanking Active TSS	K562	blood
13	chr21:45249400-45249600	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
14	chr21:45249400-45249800	Flanking Bivalent TSS/Enh	HepG2	liver
15	chr21:45249400-45250000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
16	chr21:45249400-45250600	Enhancers	Placenta	Placenta

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