Variant report

Variant	rs4275462
Chromosome Location	chr1:221902183-221902184
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:221896601..221898804-chr1:221901497..221903460,2	K562	blood:
2	chr1:221899643..221902280-chr1:221903912..221907018,3	K562	blood:
3	chr1:221900620..221902911-chr1:221912175..221914927,2	MCF-7	breast:
4	chr1:221900354..221903760-chr1:221903849..221908437,4	MCF-7	breast:

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10863650	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs12027098	0.92[ASN][1000 genomes]
rs12030765	0.92[ASN][1000 genomes]
rs12030868	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12034061	0.92[ASN][1000 genomes]
rs12034850	0.92[ASN][1000 genomes]
rs12036163	1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12041033	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12042829	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12044821	1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12116804	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12129426	0.91[EUR][1000 genomes]
rs12134197	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs12134869	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6670514	0.82[JPT][hapmap]
rs6689267	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs6693577	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7534227	0.91[EUR][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	nsv469786	chr1:221855871-222040335	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv482867	chr1:221855871-222040335	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1002463	chr1:221863355-222095773	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv535302	chr1:221863355-222095773	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv1007092	chr1:221883491-221958279	Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv535303	chr1:221883491-221958279	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4275462	TGFB2	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:221879600-221902400	Enhancers	Brain Substantia Nigra	brain
2	chr1:221888000-221903000	Enhancers	Brain Hippocampus Middle	brain
3	chr1:221890800-221906400	Weak transcription	Right Ventricle	heart
4	chr1:221890800-221910200	Weak transcription	Lung	lung
5	chr1:221891800-221911000	Weak transcription	Gastric	stomach
6	chr1:221891800-221913000	Weak transcription	Fetal Intestine Large	intestine
7	chr1:221893000-221913600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:221896600-221903200	Weak transcription	Fetal Stomach	stomach
9	chr1:221897000-221903600	Weak transcription	Left Ventricle	heart
10	chr1:221897200-221907800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:221897200-221914200	Weak transcription	Aorta	Aorta
12	chr1:221897400-221908800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr1:221897400-221913400	Weak transcription	HepG2	liver
14	chr1:221897600-221902600	Weak transcription	Fetal Lung	lung
15	chr1:221897600-221903600	Weak transcription	Fetal Muscle Trunk	muscle
16	chr1:221897600-221906800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr1:221897600-221908000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:221897600-221910200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr1:221897800-221903600	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr1:221897800-221904000	Genic enhancers	HMEC	breast
21	chr1:221898000-221903200	Enhancers	Rectal Smooth Muscle	rectum
22	chr1:221898000-221904000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:221898000-221906400	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr1:221898200-221903400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr1:221898400-221903600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr1:221898400-221903800	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr1:221898600-221902600	Enhancers	Primary T cells from cord blood	blood
28	chr1:221898600-221903200	Weak transcription	Fetal Muscle Leg	muscle
29	chr1:221898600-221903800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr1:221898600-221904000	Enhancers	Primary T helper cells PMA-I stimulated	--
31	chr1:221898600-221905800	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr1:221898600-221913600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr1:221899000-221902400	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr1:221899000-221902400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr1:221899200-221902400	Enhancers	Dnd41	blood
36	chr1:221899200-221903600	Weak transcription	Brain Germinal Matrix	brain
37	chr1:221899400-221902200	Weak transcription	HSMMtube	muscle
38	chr1:221899400-221903600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr1:221899400-221903600	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr1:221899400-221912400	Weak transcription	Esophagus	oesophagus
41	chr1:221899600-221906200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr1:221899600-221906400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr1:221899600-221908000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr1:221899600-221912400	Weak transcription	Thymus	Thymus
45	chr1:221899800-221904000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr1:221899800-221904000	Enhancers	Colon Smooth Muscle	Colon
47	chr1:221899800-221906200	Weak transcription	Adipose Nuclei	Adipose
48	chr1:221899800-221909600	Weak transcription	K562	blood
49	chr1:221899800-221910800	Weak transcription	NH-A	brain
50	chr1:221900000-221904000	Genic enhancers	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links