Variant report

Variant	rs3821217
Chromosome Location	chr2:20818286-20818287
allele	G/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:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:20804020..20806157-chr2:20816542..20819817,4	MCF-7	breast:
2	chr2:20816799..20818621-chr2:20832721..20834434,2	MCF-7	breast:
3	chr2:20816763..20821100-chr2:20824834..20828532,5	K562	blood:
4	chr2:20798546..20802204-chr2:20815122..20819483,4	MCF-7	breast:
5	chr2:20665733..20672605-chr2:20815236..20823686,12	MCF-7	breast:
6	chr2:20801637..20803782-chr2:20817932..20820325,2	MCF-7	breast:
7	chr2:20811207..20813551-chr2:20816352..20818633,2	K562	blood:
8	chr2:20789997..20792343-chr2:20817909..20819855,2	MCF-7	breast:
9	chr1:94311964..94312508-chr2:20817312..20818299,2	Hela-S3	cervix:
10	chr2:20671303..20674787-chr2:20817796..20820495,3	MCF-7	breast:
11	chr2:20644675..20653597-chr2:20811663..20819940,20	MCF-7	breast:
12	chr2:20697592..20700414-chr2:20816626..20820638,4	MCF-7	breast:
13	chr2:20817280..20821353-chr2:20848044..20851873,4	MCF-7	breast:
14	chr2:20818029..20819883-chr2:20821089..20823704,2	K562	blood:
15	chr2:20640108..20658716-chr2:20812153..20855311,258	MCF-7	breast:
16	chr2:20807683..20810867-chr2:20811760..20818347,7	MCF-7	breast:
17	chr2:20776319..20778530-chr2:20816686..20818367,2	K562	blood:
18	chr2:20752219..20755143-chr2:20816500..20818768,2	MCF-7	breast:
19	chr2:20673594..20675503-chr2:20817763..20819423,2	MCF-7	breast:
20	chr16:2204905..2206890-chr2:20817746..20820102,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000131653	Chromatin interaction
ENSG00000118960	Chromatin interaction
ENSG00000231948	Chromatin interaction
ENSG00000228950	Chromatin interaction
ENSG00000206630	Chromatin interaction
ENSG00000143878	Chromatin interaction
ENSG00000211575	Chromatin interaction
ENSG00000260260	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1047176	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11676170	1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11678019	0.89[CEU][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11688002	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs12470344	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13030108	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3732149	0.95[CEU][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732152	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732154	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3732157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796065	0.95[CEU][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55788833	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56096206	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56174003	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56203116	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56240532	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56336286	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6531247	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6719474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6721558	0.94[CEU][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6723273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6728166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72782378	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72782380	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72782396	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72784306	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7559305	0.95[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7586298	0.95[CEU][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7609280	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs896733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833537	chr2:20630092-20826816	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv833548	chr2:20682073-20864078	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1012037	chr2:20770850-20824893	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv535598	chr2:20770850-20824893	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv581167	chr2:20791125-20827846	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active 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	10 gene(s)	inside rSNPs	diseases
6	nsv1008473	chr2:20811359-20879186	Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Enhancers Flanking Active TSS Strong transcription 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	24 gene(s)	inside rSNPs	diseases
7	nsv535599	chr2:20811359-20879186	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	nsv517472	chr2:20814583-20855176	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised 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	20 gene(s)	inside rSNPs	diseases
9	nsv873725	chr2:20814583-20855176	Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3821217	HS1BP3	cis	multi-tissue	Pritchard

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20808400-20819600	Enhancers	Fetal Muscle Leg	muscle
2	chr2:20808600-20818600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr2:20808600-20819400	Enhancers	Brain Anterior Caudate	brain
4	chr2:20808600-20819800	Enhancers	Brain Substantia Nigra	brain
5	chr2:20809600-20819200	Weak transcription	Primary T cells from cord blood	blood
6	chr2:20810800-20819200	Weak transcription	Primary B cells from cord blood	blood
7	chr2:20810800-20819600	Enhancers	Brain Hippocampus Middle	brain
8	chr2:20811600-20820200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr2:20812200-20819200	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr2:20812400-20820600	Enhancers	Right Ventricle	heart
11	chr2:20812400-20820800	Enhancers	Right Atrium	heart
12	chr2:20812400-20821200	Enhancers	Left Ventricle	heart
13	chr2:20812600-20819200	Enhancers	Brain Angular Gyrus	brain
14	chr2:20812800-20819400	Enhancers	Fetal Lung	lung
15	chr2:20813000-20818400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:20813000-20818400	Enhancers	Lung	lung
17	chr2:20813000-20819000	Enhancers	Fetal Muscle Trunk	muscle
18	chr2:20813000-20819200	Enhancers	Esophagus	oesophagus
19	chr2:20813000-20819200	Enhancers	Psoas Muscle	Psoas
20	chr2:20813600-20818400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr2:20813600-20818600	Enhancers	Liver	Liver
22	chr2:20813600-20818600	Enhancers	Colonic Mucosa	Colon
23	chr2:20813600-20819400	Enhancers	Rectal Mucosa Donor 31	rectum
24	chr2:20813600-20819800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr2:20813800-20819200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr2:20813800-20819600	Enhancers	Placenta	Placenta
27	chr2:20814000-20819200	Enhancers	Rectal Mucosa Donor 29	rectum
28	chr2:20814000-20819200	Flanking Active TSS	Stomach Smooth Muscle	stomach
29	chr2:20814000-20819600	Enhancers	Pancreas	Pancrea
30	chr2:20814400-20819200	Enhancers	Ovary	ovary
31	chr2:20814400-20819400	Genic enhancers	Fetal Intestine Small	intestine
32	chr2:20814800-20818400	Weak transcription	Primary B cells from peripheral blood	blood
33	chr2:20815000-20819200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr2:20815000-20831800	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr2:20815000-20847600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr2:20815400-20818400	Enhancers	HUVEC	blood vessel
37	chr2:20815600-20818400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr2:20815600-20824200	Enhancers	Fetal Heart	heart
39	chr2:20815800-20819600	Enhancers	Stomach Mucosa	stomach
40	chr2:20816000-20818400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr2:20816000-20821000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr2:20816400-20818400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr2:20816400-20818400	Enhancers	K562	blood
44	chr2:20816400-20818600	Enhancers	Brain Germinal Matrix	brain
45	chr2:20816400-20818800	Enhancers	NHLF	lung
46	chr2:20816400-20819000	Enhancers	Gastric	stomach
47	chr2:20816400-20819400	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr2:20816400-20819800	Enhancers	NHDF-Ad	bronchial
49	chr2:20816400-20821600	Enhancers	Placenta Amnion	Placenta Amnion
50	chr2:20816600-20818400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links