Variant report

Variant	rs4669456
Chromosome Location	chr2:9920739-9920740
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:9909947..9912173-chr2:9920104..9922544,2	MCF-7	breast:
2	chr2:9919839..9921691-chr2:9937191..9939012,2	MCF-7	breast:
3	chr2:9920726..9922513-chr2:10283585..10286351,2	K562	blood:
4	chr2:9913973..9917175-chr2:9918406..9921250,3	K562	blood:

Variant related genes	Relation type
ENSG00000243491	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10186112	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10929614	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11674480	0.90[ASN][1000 genomes]
rs11887400	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11896311	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12988235	0.90[ASN][1000 genomes]
rs1515326	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2357266	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2357267	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4669455	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4669460	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4669461	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6432035	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6712066	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7599932	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7605035	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469405	chr2:9814374-9964947	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv580930	chr2:9814374-9964947	Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1003026	chr2:9854939-10012516	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv470443	chr2:9857018-9975557	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv873619	chr2:9870631-9956981	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv1013969	chr2:9888703-10023951	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv873620	chr2:9906145-9951970	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv524327	chr2:9913515-9954768	Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9911800-9922400	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr2:9912400-9921200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:9912400-9923000	Weak transcription	Right Atrium	heart
4	chr2:9914800-9922600	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr2:9915000-9924800	Weak transcription	Left Ventricle	heart
6	chr2:9917800-9923600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr2:9918000-9921000	Enhancers	Fetal Thymus	thymus
8	chr2:9918000-9922600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr2:9918000-9923400	Enhancers	Fetal Intestine Large	intestine
10	chr2:9918000-9923400	Enhancers	Fetal Intestine Small	intestine
11	chr2:9918200-9921200	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr2:9918200-9921200	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr2:9918200-9924000	Enhancers	Primary T cells fromperipheralblood	blood
14	chr2:9918400-9922600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr2:9918600-9923600	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr2:9919000-9920800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr2:9919000-9920800	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr2:9919000-9921000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr2:9919000-9922600	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr2:9919000-9923400	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr2:9919200-9921000	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr2:9919200-9922200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr2:9919400-9922600	Enhancers	GM12878-XiMat	blood
24	chr2:9919400-9927000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr2:9919800-9920800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
26	chr2:9919800-9921400	Enhancers	Esophagus	oesophagus
27	chr2:9919800-9922600	Bivalent Enhancer	HepG2	liver
28	chr2:9919800-9923400	Enhancers	Placenta	Placenta
29	chr2:9920000-9921200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
30	chr2:9920200-9922200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr2:9920200-9923000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr2:9920200-9923400	Enhancers	HMEC	breast
33	chr2:9920200-9924000	Enhancers	Primary T cells from cord blood	blood
34	chr2:9920400-9921600	Weak transcription	Duodenum Mucosa	Duodenum
35	chr2:9920400-9922200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:9920400-9922600	Weak transcription	Primary hematopoietic stem cells	blood
37	chr2:9920400-9922600	Weak transcription	Adipose Nuclei	Adipose
38	chr2:9920600-9922200	Enhancers	NHEK	skin
39	chr2:9920600-9924200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood

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