Variant report

Variant	rs13430847
Chromosome Location	chr2:10562873-10562874
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:10561260..10564585-chr2:10565466..10568336,3	MCF-7	breast:
2	chr2:10551885..10553881-chr2:10561679..10563656,2	K562	blood:
3	chr2:10220036..10221885-chr2:10562802..10564829,2	K562	blood:
4	chr2:10558775..10560512-chr2:10560876..10563127,2	K562	blood:

Variant related genes	Relation type
ENSG00000205795	Chromatin interaction
ENSG00000115756	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11674615	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11686949	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11692055	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13383055	0.80[ASN][1000 genomes]
rs13383253	0.80[ASN][1000 genomes]
rs13428169	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2270304	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2270305	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3732119	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3771120	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3771121	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3821197	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55961729	0.80[ASN][1000 genomes]
rs56156675	0.80[ASN][1000 genomes]
rs56382508	0.80[ASN][1000 genomes]
rs62130191	0.80[ASN][1000 genomes]
rs9917369	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530829	chr2:10357105-10655131	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
2	nsv873643	chr2:10535481-10583160	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv873644	chr2:10537347-10576424	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv873645	chr2:10537347-10612091	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
5	nsv1007185	chr2:10540386-10791743	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	nsv873646	chr2:10550517-10612091	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10549000-10570400	Weak transcription	Psoas Muscle	Psoas
2	chr2:10549400-10563400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr2:10549600-10572400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr2:10549800-10563400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr2:10550200-10571800	Weak transcription	Small Intestine	intestine
6	chr2:10551200-10574800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr2:10551400-10564400	Weak transcription	Fetal Kidney	kidney
8	chr2:10553000-10573200	Weak transcription	K562	blood
9	chr2:10554400-10563000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr2:10554400-10566800	Weak transcription	NHLF	lung
11	chr2:10554400-10567800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:10554600-10565200	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr2:10554600-10579200	Weak transcription	NHDF-Ad	bronchial
14	chr2:10554800-10565800	Weak transcription	Aorta	Aorta
15	chr2:10554800-10572600	Weak transcription	Colon Smooth Muscle	Colon
16	chr2:10555000-10564400	Weak transcription	Hela-S3	cervix
17	chr2:10555200-10563000	Weak transcription	Fetal Brain Female	brain
18	chr2:10555200-10563200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr2:10555200-10563200	Weak transcription	Left Ventricle	heart
20	chr2:10555200-10563400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr2:10555200-10566000	Weak transcription	Brain Anterior Caudate	brain
22	chr2:10555400-10565800	Weak transcription	HMEC	breast
23	chr2:10555400-10566600	Weak transcription	Brain Germinal Matrix	brain
24	chr2:10555400-10566800	Weak transcription	Fetal Brain Male	brain
25	chr2:10555800-10572600	Weak transcription	HSMM	muscle
26	chr2:10558000-10563200	Weak transcription	A549	lung
27	chr2:10558000-10564400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:10558200-10565600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:10558200-10568600	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr2:10559000-10568000	Weak transcription	Dnd41	blood
31	chr2:10559400-10567400	Strong transcription	Fetal Stomach	stomach
32	chr2:10559400-10568200	Strong transcription	Thymus	Thymus
33	chr2:10559400-10568400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr2:10559400-10568400	Strong transcription	Liver	Liver
35	chr2:10559400-10568800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:10559400-10568800	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr2:10559400-10569000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr2:10559600-10566200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr2:10559600-10568200	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr2:10559600-10568200	Strong transcription	Gastric	stomach
41	chr2:10559600-10568400	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr2:10559600-10568400	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr2:10559600-10568400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr2:10559600-10568400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr2:10559600-10568400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr2:10559600-10568800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr2:10559600-10568800	Strong transcription	Lung	lung
48	chr2:10559600-10569000	Strong transcription	Primary T cells from cord blood	blood
49	chr2:10559800-10564600	Strong transcription	Spleen	Spleen
50	chr2:10559800-10568000	Strong transcription	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links