Variant report

Variant	rs57940327
Chromosome Location	chr3:53055599-53055600
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:53053108..53056030-chr3:53104834..53107226,3	K562	blood:
2	chr3:53055176..53056730-chr3:53078490..53080404,2	MCF-7	breast:
3	chr3:53054569..53056705-chr3:53106775..53108496,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163935	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs28696085	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28719645	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3806693	1.00[ASN][1000 genomes]
rs55794978	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55885034	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56835905	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58309671	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58840385	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59224641	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59515578	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60648378	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60744886	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61285888	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61297461	1.00[AFR][1000 genomes]
rs61437303	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61438885	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6772715	0.90[AFR][1000 genomes]
rs72961763	0.90[AFR][1000 genomes]
rs72965343	0.99[AFR][1000 genomes]
rs72965345	1.00[ASN][1000 genomes]
rs72965350	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72965354	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72965361	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72965362	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72965366	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72965381	0.84[ASN][1000 genomes]
rs7628501	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7631487	1.00[ASN][1000 genomes]
rs9819608	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9822686	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9852646	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1818974	chr3:52966316-53096394	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv876799	chr3:53024216-53060637	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv590320	chr3:53027983-53055842	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv590321	chr3:53027983-53062661	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv876800	chr3:53038786-53113762	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv1823728	chr3:53046712-53080351	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	esv1820544	chr3:53046712-53096394	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53019000-53057200	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr3:53019600-53056400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr3:53020600-53057000	Weak transcription	Dnd41	blood
4	chr3:53025600-53061600	Weak transcription	Lung	lung
5	chr3:53027600-53061600	Weak transcription	Liver	Liver
6	chr3:53030200-53059400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:53033000-53078400	Weak transcription	Aorta	Aorta
8	chr3:53033200-53057000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr3:53033600-53056200	Weak transcription	Fetal Stomach	stomach
10	chr3:53033800-53060400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:53033800-53065000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr3:53037000-53065000	Weak transcription	Fetal Intestine Small	intestine
13	chr3:53040800-53065000	Weak transcription	Fetal Intestine Large	intestine
14	chr3:53043800-53064800	Weak transcription	Stomach Mucosa	stomach
15	chr3:53044400-53056000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr3:53044600-53055600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr3:53044600-53065000	Weak transcription	Gastric	stomach
18	chr3:53045200-53061400	Weak transcription	Fetal Heart	heart
19	chr3:53045400-53057200	Weak transcription	Psoas Muscle	Psoas
20	chr3:53045400-53061600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr3:53045600-53057000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr3:53045600-53057600	Weak transcription	Left Ventricle	heart
23	chr3:53045800-53061400	Weak transcription	HepG2	liver
24	chr3:53046000-53057600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr3:53048400-53058600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr3:53048800-53077800	Weak transcription	Stomach Smooth Muscle	stomach
27	chr3:53049200-53059800	Weak transcription	Pancreas	Pancrea
28	chr3:53050600-53057200	Weak transcription	Small Intestine	intestine
29	chr3:53050600-53062000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:53051400-53056600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr3:53051800-53056800	Weak transcription	Primary hematopoietic stem cells	blood
32	chr3:53052000-53064800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr3:53052800-53056600	Weak transcription	Primary T cells from cord blood	blood
34	chr3:53052800-53057000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr3:53053000-53057200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr3:53053000-53057400	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr3:53053000-53057600	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr3:53053000-53063600	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr3:53053200-53055600	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr3:53053200-53056800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr3:53053200-53057000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr3:53053200-53057600	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr3:53053400-53058200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr3:53053800-53061600	Weak transcription	Ovary	ovary
45	chr3:53054000-53070600	Weak transcription	Right Ventricle	heart
46	chr3:53054200-53056400	Weak transcription	Primary T helper cells PMA-I stimulated	--
47	chr3:53054200-53056600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr3:53054400-53059800	Weak transcription	Primary B cells from cord blood	blood
49	chr3:53054400-53064800	Weak transcription	Primary B cells from peripheral blood	blood
50	chr3:53055400-53056000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links