Variant report

Variant	rs59929475
Chromosome Location	chr4:99197311-99197312
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	chr4:99190517..99192752-chr4:99196803..99199545,2	MCF-7	breast:
2	chr4:99190051..99193049-chr4:99195495..99197836,2	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs28651913	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2866008	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28683554	1.00[EUR][1000 genomes]
rs58408865	1.00[EUR][1000 genomes]
rs58485619	1.00[EUR][1000 genomes]
rs58977062	1.00[EUR][1000 genomes]
rs59516498	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60266816	1.00[EUR][1000 genomes]
rs60470511	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61041466	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72883608	1.00[EUR][1000 genomes]
rs72883610	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72883612	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72883618	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72892327	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72892332	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72892346	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72892347	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72892354	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72892355	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72892359	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72892365	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72892368	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72892376	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72894293	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72894299	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72894392	1.00[EUR][1000 genomes]
rs72896117	1.00[EUR][1000 genomes]
rs72896309	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72896311	1.00[EUR][1000 genomes]
rs72896316	1.00[EUR][1000 genomes]
rs72896319	1.00[EUR][1000 genomes]
rs72896324	1.00[EUR][1000 genomes]
rs72896325	1.00[EUR][1000 genomes]
rs72896335	1.00[EUR][1000 genomes]
rs72896338	1.00[EUR][1000 genomes]
rs72896342	1.00[EUR][1000 genomes]
rs72896346	1.00[EUR][1000 genomes]
rs72896356	1.00[EUR][1000 genomes]
rs72896358	1.00[EUR][1000 genomes]
rs72896365	1.00[EUR][1000 genomes]
rs72896389	1.00[EUR][1000 genomes]
rs72896392	1.00[EUR][1000 genomes]
rs72898108	1.00[EUR][1000 genomes]
rs72898341	1.00[EUR][1000 genomes]
rs72898343	1.00[EUR][1000 genomes]
rs72898363	1.00[EUR][1000 genomes]
rs72898376	1.00[EUR][1000 genomes]
rs72898388	1.00[EUR][1000 genomes]
rs72898393	1.00[EUR][1000 genomes]
rs72900361	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72900365	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72900388	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72900390	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	nsv529623	chr4:98501338-99460166	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv1001570	chr4:98976239-99239838	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv1004616	chr4:99085875-99308901	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv2763801	chr4:99094892-99413853	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv2754250	chr4:99094922-99527122	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv879651	chr4:99105055-99441349	Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv879652	chr4:99125659-99303633	Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv528127	chr4:99146436-99229839	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking 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
9	nsv879653	chr4:99152631-99260423	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99183600-99198200	Weak transcription	Ovary	ovary
2	chr4:99183600-99205400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr4:99184000-99205800	Weak transcription	Gastric	stomach
4	chr4:99184000-99210400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr4:99184000-99239600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr4:99184200-99199000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr4:99184200-99205800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr4:99184200-99205800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr4:99184200-99210000	Weak transcription	HSMMtube	muscle
10	chr4:99184200-99242200	Weak transcription	A549	lung
11	chr4:99184600-99205800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr4:99184600-99211800	Weak transcription	NHLF	lung
13	chr4:99185000-99197800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr4:99185000-99199600	Weak transcription	NHDF-Ad	bronchial
15	chr4:99185000-99204400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr4:99185000-99206600	Weak transcription	NH-A	brain
17	chr4:99185200-99205600	Weak transcription	HMEC	breast
18	chr4:99185400-99239400	Weak transcription	NHEK	skin
19	chr4:99186200-99205800	Weak transcription	HUVEC	blood vessel
20	chr4:99186600-99210000	Weak transcription	K562	blood
21	chr4:99187000-99202800	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr4:99189600-99204200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr4:99191800-99199400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr4:99192000-99205800	Weak transcription	Psoas Muscle	Psoas
25	chr4:99193800-99197400	Weak transcription	HSMM	muscle
26	chr4:99194000-99215400	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr4:99194400-99204200	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr4:99194400-99205800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr4:99194400-99206000	Weak transcription	Aorta	Aorta
30	chr4:99194600-99214600	Weak transcription	Liver	Liver
31	chr4:99196000-99204400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr4:99196200-99197400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr4:99196200-99198400	Strong transcription	Primary B cells from cord blood	blood
34	chr4:99196400-99197600	ZNF genes & repeats	Primary T cells from cord blood	blood
35	chr4:99196400-99204000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr4:99196600-99214200	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr4:99196800-99197400	Strong transcription	Fetal Thymus	thymus
38	chr4:99196800-99197600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr4:99197000-99197400	ZNF genes & repeats	Fetal Muscle Leg	muscle
40	chr4:99197000-99197400	ZNF genes & repeats	Left Ventricle	heart
41	chr4:99197000-99197600	Strong transcription	Primary B cells from peripheral blood	blood
42	chr4:99197000-99197600	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr4:99197000-99214600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr4:99197200-99197400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
45	chr4:99197200-99197400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr4:99197200-99197400	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr4:99197200-99198000	Weak transcription	Dnd41	blood
48	chr4:99197200-99198400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr4:99197200-99198600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links