Variant report

Variant	rs2838716
Chromosome Location	chr21:46285026-46285027
allele	A/G
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	POLR2A	chr21:46284373-46285144	HepG2	liver:	n/a	n/a
2	MAX	chr21:46285011-46285886	MCF-7	breast:	n/a	chr21:46285293-46285304 chr21:46285294-46285304 chr21:46285294-46285303 chr21:46285295-46285302 chr21:46285840-46285849

No.	Distal block	Cell Line	Cell type
1	chr21:46280368..46282945-chr21:46283456..46285604,4	MCF-7	breast:
2	chr21:46234824..46239565-chr21:46284858..46289652,5	K562	blood:
3	chr21:46237330..46240146-chr21:46282395..46285243,3	K562	blood:
4	chr21:46282547..46285422-chr21:46309419..46311568,2	K562	blood:
5	chr21:45930623..45933218-chr21:46282665..46285532,2	MCF-7	breast:
6	chr21:46274905..46276457-chr21:46283894..46285475,2	K562	blood:
7	chr21:46220733..46222651-chr21:46282710..46285466,2	K562	blood:
8	chr21:46283208..46285602-chr21:46427466..46429012,2	MCF-7	breast:
9	chr21:46236678..46239215-chr21:46284689..46286960,3	MCF-7	breast:

Variant related genes	Relation type
PTTG1IP	TF binding region
ENSG00000184787	Chromatin interaction
ENSG00000184900	Chromatin interaction
ENSG00000236519	Chromatin interaction
ENSG00000183255	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs173098	0.88[ASN][1000 genomes]
rs183519	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1970054	1.00[JPT][hapmap]
rs235260	0.86[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap]
rs235265	0.86[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs235303	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs235306	0.92[ASN][1000 genomes]
rs235318	0.81[GIH][hapmap]
rs235320	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs235322	1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.92[ASN][1000 genomes]
rs235370	0.94[ASW][hapmap];0.88[CHB][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];0.81[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs235372	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs235375	0.92[ASN][1000 genomes]
rs2838717	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2838718	0.86[AMR][1000 genomes]
rs2838726	1.00[JPT][hapmap]
rs2838727	1.00[JPT][hapmap]
rs3788142	1.00[JPT][hapmap]
rs684	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7282839	1.00[JPT][hapmap]
rs741951	0.88[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916258	chr21:45995986-46624705	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
2	nsv1062245	chr21:46096964-46332587	Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv544478	chr21:46096964-46332587	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv913964	chr21:46223847-46298869	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv913962	chr21:46223847-46321172	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv913965	chr21:46223847-46321172	Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	nsv1058550	chr21:46227163-46317934	Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	nsv913968	chr21:46249752-46301008	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv1060233	chr21:46254075-46323401	Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
10	nsv1056513	chr21:46254075-46442759	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
11	nsv913969	chr21:46279505-46472929	Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
12	nsv544479	chr21:46280467-46323401	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
13	nsv470907	chr21:46283669-46306161	Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
14	nsv459299	chr21:46283669-46311264	Strong transcription Active TSS Genic enhancers Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
15	nsv459300	chr21:46283669-46311264	Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
16	nsv587814	chr21:46283669-46311264	Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2838716	RGS1	trans	lymphoblastoid	seeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46267400-46285200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr21:46267400-46286600	Strong transcription	Fetal Stomach	stomach
3	chr21:46267600-46287000	Strong transcription	Brain Germinal Matrix	brain
4	chr21:46268200-46285800	Strong transcription	Fetal Muscle Leg	muscle
5	chr21:46268600-46285200	Strong transcription	Muscle Satellite Cultured Cells	--
6	chr21:46268600-46285200	Strong transcription	Osteobl	bone
7	chr21:46268600-46285400	Strong transcription	Thymus	Thymus
8	chr21:46268600-46285400	Strong transcription	HUVEC	blood vessel
9	chr21:46268600-46285800	Strong transcription	Liver	Liver
10	chr21:46268600-46286000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr21:46268600-46286600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr21:46268800-46285200	Strong transcription	Dnd41	blood
13	chr21:46268800-46285200	Strong transcription	NHLF	lung
14	chr21:46268800-46285400	Strong transcription	Duodenum Smooth Muscle	Duodenum
15	chr21:46268800-46286600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr21:46268800-46286600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr21:46268800-46286600	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr21:46269400-46285800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr21:46271400-46286800	Weak transcription	Psoas Muscle	Psoas
20	chr21:46272600-46285200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr21:46273000-46286600	Strong transcription	H9 Cell Line	embryonic stem cell
22	chr21:46273400-46285600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr21:46274200-46285200	Strong transcription	Fetal Intestine Small	intestine
24	chr21:46274400-46285400	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr21:46275600-46290600	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr21:46275800-46285200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr21:46276400-46285200	Strong transcription	Fetal Thymus	thymus
28	chr21:46276400-46286000	Strong transcription	K562	blood
29	chr21:46277800-46286600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr21:46278200-46285600	Strong transcription	Aorta	Aorta
31	chr21:46278200-46286400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
32	chr21:46278400-46289600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr21:46279400-46286600	Weak transcription	Fetal Brain Male	brain
34	chr21:46279400-46288400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr21:46279600-46285200	Strong transcription	Adipose Nuclei	Adipose
36	chr21:46279600-46288800	Weak transcription	Fetal Kidney	kidney
37	chr21:46279800-46285200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr21:46279800-46287600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr21:46280600-46285600	Genic enhancers	Primary T cells fromperipheralblood	blood
40	chr21:46280800-46285400	Weak transcription	NH-A	brain
41	chr21:46281000-46285600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr21:46281400-46285400	Strong transcription	Brain Cingulate Gyrus	brain
43	chr21:46281400-46286000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr21:46281800-46285200	Strong transcription	Fetal Lung	lung
45	chr21:46282000-46285800	Strong transcription	A549	lung
46	chr21:46282000-46286000	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr21:46282200-46285800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr21:46282200-46286000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr21:46282200-46286200	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr21:46282800-46285200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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