Variant report

Variant	rs58696000
Chromosome Location	chr2:20824186-20824187
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:20643596..20652981-chr2:20820571..20828990,20	MCF-7	breast:
2	chr2:20640108..20658716-chr2:20812153..20855311,258	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228950	Chromatin interaction
ENSG00000143878	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10176721	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10200826	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10201427	1.00[EUR][1000 genomes]
rs10203073	1.00[EUR][1000 genomes]
rs11893093	1.00[EUR][1000 genomes]
rs1437408	1.00[EUR][1000 genomes]
rs16988071	1.00[EUR][1000 genomes]
rs28488411	0.85[AMR][1000 genomes]
rs28529647	0.85[AMR][1000 genomes]
rs28600892	0.85[AMR][1000 genomes]
rs28642817	0.85[AMR][1000 genomes]
rs340605	1.00[EUR][1000 genomes]
rs340608	1.00[EUR][1000 genomes]
rs548324	1.00[EUR][1000 genomes]
rs553687	1.00[EUR][1000 genomes]
rs55751815	0.85[AMR][1000 genomes]
rs56737091	1.00[EUR][1000 genomes]
rs571566	1.00[EUR][1000 genomes]
rs57494499	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57524662	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs582107	1.00[EUR][1000 genomes]
rs58590712	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59300971	0.85[AMR][1000 genomes]
rs59771803	0.85[AMR][1000 genomes]
rs59882809	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60283906	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61478003	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs642152	1.00[EUR][1000 genomes]
rs648568	1.00[EUR][1000 genomes]
rs662193	1.00[EUR][1000 genomes]
rs6736533	1.00[EUR][1000 genomes]
rs6759981	1.00[EUR][1000 genomes]
rs73224614	1.00[EUR][1000 genomes]
rs73235054	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73235057	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73235060	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73235063	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73235064	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73235072	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73235079	1.00[EUR][1000 genomes]
rs73235100	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73237114	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73237122	0.91[AFR][1000 genomes]
rs73237135	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73237147	1.00[EUR][1000 genomes]
rs73919913	0.85[AMR][1000 genomes]
rs73919915	0.85[AMR][1000 genomes]
rs73919918	0.85[AMR][1000 genomes]
rs73919920	0.85[AMR][1000 genomes]
rs73919921	0.85[AMR][1000 genomes]
rs73919922	0.85[AMR][1000 genomes]
rs73919924	0.85[AMR][1000 genomes]
rs7564684	0.85[AMR][1000 genomes]
rs7574045	0.85[AMR][1000 genomes]
rs7574289	0.85[AMR][1000 genomes]
rs7601273	0.85[AMR][1000 genomes]
rs839914	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
10	nsv527901	chr2:20818458-20876386	Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20815000-20831800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr2:20815000-20847600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:20815600-20824200	Enhancers	Fetal Heart	heart
4	chr2:20817000-20824200	Weak transcription	Thymus	Thymus
5	chr2:20817200-20826600	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr2:20817400-20827200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr2:20817400-20831400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:20817400-20835200	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr2:20817400-20847600	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr2:20817600-20832200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr2:20817600-20850000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr2:20817800-20826200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr2:20817800-20833800	Weak transcription	Fetal Thymus	thymus
14	chr2:20818000-20825600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr2:20818200-20825200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr2:20818200-20828600	Weak transcription	Fetal Kidney	kidney
17	chr2:20818200-20835000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr2:20818200-20835000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr2:20818400-20825000	Strong transcription	Primary B cells from peripheral blood	blood
20	chr2:20818400-20825600	Weak transcription	HUVEC	blood vessel
21	chr2:20818400-20828800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr2:20818400-20828800	Weak transcription	Fetal Brain Male	brain
23	chr2:20818400-20831800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr2:20818600-20824800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr2:20818600-20825600	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr2:20818800-20824800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr2:20818800-20825200	Strong transcription	Sigmoid Colon	Sigmoid Colon
28	chr2:20818800-20826200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
29	chr2:20818800-20833600	Weak transcription	A549	lung
30	chr2:20818800-20842400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr2:20819000-20847400	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr2:20819200-20824600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr2:20819200-20825000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr2:20819200-20825400	Strong transcription	Primary B cells from cord blood	blood
35	chr2:20819200-20826200	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr2:20819200-20827000	Strong transcription	Primary T cells from cord blood	blood
37	chr2:20819200-20827200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr2:20819400-20824400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr2:20819400-20824800	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr2:20819400-20825000	Strong transcription	NHLF	lung
41	chr2:20819400-20825600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr2:20819400-20834200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr2:20819400-20847800	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr2:20819600-20824600	Strong transcription	Brain Germinal Matrix	brain
45	chr2:20819600-20825000	Strong transcription	Duodenum Mucosa	Duodenum
46	chr2:20819600-20825200	Strong transcription	Colonic Mucosa	Colon
47	chr2:20819600-20825200	Genic enhancers	Fetal Muscle Leg	muscle
48	chr2:20819600-20825600	Strong transcription	Pancreas	Pancrea
49	chr2:20819800-20824600	Strong transcription	Primary T helper cells PMA-I stimulated	--
50	chr2:20819800-20824600	Strong transcription	Liver	Liver

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