Variant report

Variant	rs2007462
Chromosome Location	chr2:47229025-47229026
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RFX5	chr2:47228920-47231067	SK-N-SH	brain:	n/a	chr2:47229898-47229913 chr2:47229895-47229910 chr2:47229899-47229908 chr2:47229897-47229914 chr2:47229214-47229231 chr2:47229898-47229913 chr2:47229923-47229938 chr2:47229896-47229910 chr2:47229898-47229913 chr2:47229897-47229905 chr2:47229926-47229935
2	MXI1	chr2:47228934-47230772	SK-N-SH	brain:	n/a	chr2:47229899-47229914 chr2:47229897-47229912

No.	Distal block	Cell Line	Cell type
1	chr2:47227819..47229844-chr2:47253559..47255515,2	K562	blood:
2	chr2:47226708..47229516-chr2:47234175..47237170,3	K562	blood:
3	chr2:47226060..47229055-chr2:47402454..47404695,2	K562	blood:
4	chr2:47227228..47229377-chr2:47229384..47232229,2	K562	blood:

Variant related genes	Relation type
TTC7A	TF binding region
ENSG00000143933	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs17481349	0.96[AFR][1000 genomes]
rs17540003	0.80[YRI][hapmap]
rs17540504	0.82[EUR][1000 genomes]
rs17540615	0.92[CEU][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55944397	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72872910	0.96[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7581528	0.92[CEU][hapmap];0.88[AMR][1000 genomes];0.90[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	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
5	nsv524970	chr2:47162739-47302095	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1000377	chr2:47189386-47344029	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv581750	chr2:47207665-47229953	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv525197	chr2:47210747-47297973	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv517929	chr2:47217094-47243312	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	nsv518312	chr2:47224927-47262137	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47213600-47256400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:47214000-47262000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:47214200-47231000	Weak transcription	K562	blood
4	chr2:47214200-47235400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr2:47214600-47242000	Strong transcription	Thymus	Thymus
6	chr2:47214800-47229400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr2:47214800-47229600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr2:47214800-47230400	Strong transcription	Osteobl	bone
9	chr2:47214800-47231200	Weak transcription	HUVEC	blood vessel
10	chr2:47214800-47233400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr2:47214800-47237200	Strong transcription	Primary T cells from cord blood	blood
12	chr2:47214800-47239200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr2:47215200-47243800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr2:47215400-47235800	Strong transcription	Primary B cells from cord blood	blood
15	chr2:47215600-47245200	Strong transcription	Primary B cells from peripheral blood	blood
16	chr2:47216400-47241600	Strong transcription	Fetal Thymus	thymus
17	chr2:47216600-47229400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr2:47218400-47229400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr2:47219000-47229600	Strong transcription	Spleen	Spleen
20	chr2:47219600-47235400	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr2:47221600-47229600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr2:47222000-47260600	Weak transcription	Small Intestine	intestine
23	chr2:47222600-47229800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr2:47223200-47229600	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr2:47223200-47235800	Weak transcription	Fetal Kidney	kidney
26	chr2:47223400-47229200	Weak transcription	Fetal Brain Male	brain
27	chr2:47223400-47229800	Weak transcription	Hela-S3	cervix
28	chr2:47223400-47238400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr2:47223400-47239400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr2:47223600-47235600	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr2:47223600-47239400	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr2:47223600-47246800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr2:47223800-47229200	Weak transcription	Ovary	ovary
34	chr2:47223800-47229600	Weak transcription	Right Ventricle	heart
35	chr2:47223800-47234200	Weak transcription	Psoas Muscle	Psoas
36	chr2:47224000-47229600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr2:47224000-47229600	Weak transcription	Colonic Mucosa	Colon
38	chr2:47224200-47233200	Weak transcription	GM12878-XiMat	blood
39	chr2:47224400-47229800	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr2:47224600-47229200	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr2:47224800-47238400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr2:47225000-47229600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr2:47225000-47229800	Weak transcription	NH-A	brain
44	chr2:47225400-47229600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr2:47225800-47229200	Weak transcription	Stomach Mucosa	stomach
46	chr2:47226000-47229800	Weak transcription	NHEK	skin
47	chr2:47226600-47229400	Weak transcription	HSMMtube	muscle
48	chr2:47226600-47229600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr2:47226600-47233000	Weak transcription	Liver	Liver
50	chr2:47226800-47229200	Weak transcription	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links