Variant report

Variant	rs9974152
Chromosome Location	chr21:46353985-46353986
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr21:46353396-46355647	GM12878	blood:	n/a	n/a
2	POLR2A	chr21:46346154-46355833	GM19099	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr21:46348854..46378176-chr21:46489799..46500436,75	K562	blood:
2	chr21:46310744..46314052-chr21:46353302..46357037,3	K562	blood:
3	chr21:46221821..46223623-chr21:46352044..46354784,3	MCF-7	breast:
4	chr21:46353923..46356909-chr21:46357554..46361249,6	K562	blood:
5	chr21:46233611..46237296-chr21:46352613..46355418,3	K562	blood:
6	chr21:46230539..46232494-chr21:46352107..46354258,2	K562	blood:
7	chr21:46220228..46226309-chr21:46349546..46355767,8	K562	blood:
8	chr21:46288744..46296879-chr21:46346201..46354260,26	MCF-7	breast:
9	chr21:46352341..46354807-chr21:46362095..46363713,2	K562	blood:
10	chr21:46352849..46354653-chr21:46493857..46495814,2	K562	blood:
11	chr21:46344850..46350559-chr21:46353409..46355667,8	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C21orf67-6	chr21:46353199-46354283	NR_027128

No data

Variant related genes	Relation type
ENSG00000273027	TF binding region
ITGB2	TF binding region
ENSG00000272825	TF binding region
ENSG00000197381	Chromatin interaction
ENSG00000160256	Chromatin interaction
ENSG00000273027	Chromatin interaction
ENSG00000268856	Chromatin interaction
ENSG00000160255	Chromatin interaction
ENSG00000184787	Chromatin interaction
ENSG00000236519	Chromatin interaction
ENSG00000235374	Chromatin interaction
ENSG00000183255	Chromatin interaction
ENSG00000183250	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10775679	0.96[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11088970	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11088972	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11088973	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11701017	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11701173	0.84[ASN][1000 genomes]
rs11701737	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12106389	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12626600	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs13046102	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2294169	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2838749	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3827260	0.96[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.83[ASN][1000 genomes]
rs4818745	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4818989	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4818991	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4818992	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4818998	0.96[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4819000	0.96[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56122469	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56199687	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7277732	0.92[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs7278544	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7278847	0.96[CEU][hapmap];0.90[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7283236	1.00[ASW][hapmap];0.96[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs883907	0.88[CEU][hapmap];0.87[CHB][hapmap]
rs883908	0.87[CHB][hapmap]
rs9974072	0.96[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9974593	0.96[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9976402	0.96[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 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	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
3	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
4	nsv913970	chr21:46305175-46487831	Bivalent Enhancer Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv933240	chr21:46305956-46371518	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv913974	chr21:46306161-46430792	Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv913975	chr21:46306161-46459432	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
8	nsv913976	chr21:46306161-46487831	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	nsv834110	chr21:46316183-46505151	Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
10	nsv1064518	chr21:46317690-46413159	Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
11	nsv913977	chr21:46335761-46454391	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
12	nsv913978	chr21:46335761-46466674	Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
13	nsv913979	chr21:46335761-46472929	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
14	nsv913980	chr21:46337565-46454391	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
15	nsv913981	chr21:46344426-46408790	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
16	nsv913982	chr21:46344426-46430792	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
17	nsv913984	chr21:46344426-46435610	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
18	nsv913983	chr21:46344426-46440385	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
19	nsv913985	chr21:46344426-46448142	Weak transcription Genic enhancers Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
20	nsv913986	chr21:46344426-46466674	Strong transcription Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
21	nsv913987	chr21:46344426-46472929	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
22	esv1808790	chr21:46349496-46355712	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9974152	C21orf69	cis	multi-tissue	Pritchard

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46352400-46354800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
2	chr21:46352600-46354600	Bivalent Enhancer	Fetal Muscle Leg	muscle
3	chr21:46352800-46358400	Weak transcription	HMEC	breast
4	chr21:46353000-46354000	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr21:46353000-46354200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
6	chr21:46353000-46354600	Enhancers	HepG2	liver
7	chr21:46353000-46355800	Enhancers	Fetal Thymus	thymus
8	chr21:46353000-46358600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr21:46353000-46358800	Weak transcription	Right Ventricle	heart
10	chr21:46353000-46359000	Weak transcription	Brain Anterior Caudate	brain
11	chr21:46353000-46359000	Weak transcription	Right Atrium	heart
12	chr21:46353200-46354000	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
13	chr21:46353200-46354000	Enhancers	Primary B cells from peripheral blood	blood
14	chr21:46353200-46355400	Enhancers	Thymus	Thymus
15	chr21:46353200-46358600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr21:46353200-46358600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr21:46353200-46358800	Weak transcription	Pancreas	Pancrea
18	chr21:46353200-46359000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr21:46353200-46359000	Weak transcription	HUVEC	blood vessel
20	chr21:46353200-46359200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr21:46353400-46354000	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr21:46353400-46358800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr21:46353400-46358800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr21:46353400-46358800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr21:46353400-46359000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr21:46353400-46359200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr21:46353600-46354000	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr21:46353600-46354200	Genic enhancers	Monocytes-CD14+_RO01746	blood
29	chr21:46353600-46358600	Weak transcription	Liver	Liver
30	chr21:46353600-46358800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr21:46353600-46358800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr21:46353600-46358800	Weak transcription	Spleen	Spleen
33	chr21:46353600-46359000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr21:46353600-46359200	Weak transcription	Primary T cells from cord blood	blood
35	chr21:46353800-46354000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
36	chr21:46353800-46354000	Active TSS	GM12878-XiMat	blood
37	chr21:46353800-46355400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr21:46353800-46358800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr21:46353800-46358800	Weak transcription	Primary B cells from cord blood	blood
40	chr21:46353800-46358800	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr21:46353800-46358800	Weak transcription	Gastric	stomach
42	chr21:46353800-46358800	Weak transcription	HSMM	muscle
43	chr21:46353800-46358800	Weak transcription	Osteobl	bone
44	chr21:46353800-46359000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr21:46353800-46359000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
46	chr21:46353800-46359000	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr21:46353800-46359000	Weak transcription	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links