Variant report

Variant	rs12508269
Chromosome Location	chr4:104000922-104000923
allele	C/T
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	E2F4	chr4:104000850-104000936	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:103939290..103941990-chr4:103997804..104000978,3	K562	blood:
2	chr4:103996451..103999149-chr4:103999311..104004368,5	MCF-7	breast:
3	chr4:104000908..104002877-chr4:104007976..104009657,2	K562	blood:
4	chr4:103995898..104000159-chr4:104000809..104003700,8	K562	blood:

Variant related genes	Relation type
SLC9B2	TF binding region
ENSG00000164038	Chromatin interaction
ENSG00000164037	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10516498	0.93[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.97[ASN][1000 genomes]
rs1054707	0.97[ASN][1000 genomes]
rs11724309	0.88[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs11724466	0.97[ASN][1000 genomes]
rs11724522	0.97[ASN][1000 genomes]
rs11725048	0.88[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];0.91[ASN][1000 genomes]
rs11726284	0.86[CHB][hapmap];0.94[GIH][hapmap];0.87[MKK][hapmap];1.00[AFR][1000 genomes]
rs11727029	0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs11729856	0.85[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs11730764	0.97[ASN][1000 genomes]
rs11730765	0.97[ASN][1000 genomes]
rs11734318	0.94[ASN][1000 genomes]
rs11737673	0.86[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs12500173	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12500951	0.97[ASN][1000 genomes]
rs12504143	0.88[ASN][1000 genomes]
rs12504262	0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs12505289	0.97[ASN][1000 genomes]
rs12505908	0.88[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs12506065	0.88[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];0.97[ASN][1000 genomes]
rs12506157	0.88[CHB][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs12506198	0.88[CHB][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs12507348	0.88[CHB][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs12511516	0.91[ASN][1000 genomes]
rs12512468	1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs1381657	0.88[CHB][hapmap];0.92[JPT][hapmap]
rs1381658	0.94[ASN][1000 genomes]
rs17215694	0.88[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.92[MEX][hapmap];0.97[ASN][1000 genomes]
rs17215785	0.97[ASN][1000 genomes]
rs17215862	0.88[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs17217431	0.88[CHB][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs17217592	0.88[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap];0.90[ASN][1000 genomes]
rs17283027	0.88[ASN][1000 genomes]
rs17283077	0.88[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs17283194	0.88[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs17522932	0.97[ASN][1000 genomes]
rs2306478	0.88[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[ASN][1000 genomes]
rs2720469	0.81[CHD][hapmap]
rs2866633	0.97[ASN][1000 genomes]
rs35714833	0.97[ASN][1000 genomes]
rs3756268	0.88[CHB][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs3756269	0.88[CHB][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs3765086	0.88[CHB][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];0.88[ASN][1000 genomes]
rs3775972	0.88[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[ASN][1000 genomes]
rs3796982	0.86[CHB][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs3796983	0.93[CHD][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs3974474	0.88[CHB][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs55895342	0.88[ASN][1000 genomes]
rs56126326	0.97[ASN][1000 genomes]
rs56256243	0.91[ASN][1000 genomes]
rs56378042	0.88[ASN][1000 genomes]
rs56412006	0.94[ASN][1000 genomes]
rs58648171	0.91[ASN][1000 genomes]
rs58888668	0.89[ASN][1000 genomes]
rs59192877	0.90[ASN][1000 genomes]
rs59341670	0.89[ASN][1000 genomes]
rs61355145	0.97[ASN][1000 genomes]
rs6533057	0.86[ASN][1000 genomes]
rs66869812	0.91[ASN][1000 genomes]
rs6822891	0.85[ASN][1000 genomes]
rs6825519	0.93[CHD][hapmap];0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs6830791	0.97[ASN][1000 genomes]
rs6836162	0.97[ASN][1000 genomes]
rs6837114	0.90[ASN][1000 genomes]
rs6840401	0.97[ASN][1000 genomes]
rs72665040	0.97[ASN][1000 genomes]
rs72665042	0.97[ASN][1000 genomes]
rs72665048	0.97[ASN][1000 genomes]
rs72665052	0.97[ASN][1000 genomes]
rs72665054	0.97[ASN][1000 genomes]
rs72665056	0.97[ASN][1000 genomes]
rs72665063	0.94[ASN][1000 genomes]
rs72665071	0.91[ASN][1000 genomes]
rs72665093	0.88[ASN][1000 genomes]
rs72665096	0.88[ASN][1000 genomes]
rs72666812	0.90[ASN][1000 genomes]
rs736048	0.97[ASN][1000 genomes]
rs746829	0.88[CHB][hapmap];0.93[CHD][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]
rs7662455	0.87[ASN][1000 genomes]
rs7664021	0.94[ASN][1000 genomes]
rs7666067	0.88[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[ASN][1000 genomes]
rs7668568	0.88[CHB][hapmap];0.81[GIH][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];0.97[ASN][1000 genomes]
rs7675057	0.82[CHD][hapmap];0.85[JPT][hapmap];0.93[ASN][1000 genomes]
rs7686105	0.94[ASN][1000 genomes]
rs7690059	0.88[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];0.92[JPT][hapmap];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757946	chr4:103780705-104057321	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2759270	chr4:103780705-104057321	ZNF genes & repeats Strong transcription Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv3429917	chr4:103915319-104207455	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv830021	chr4:103934454-104100588	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103997800-104007800	Weak transcription	Spleen	Spleen
2	chr4:103998000-104007600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:103998200-104003200	Weak transcription	Fetal Kidney	kidney
4	chr4:103998200-104007000	Weak transcription	Lung	lung
5	chr4:103998200-104007200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr4:103998200-104007200	Weak transcription	Thymus	Thymus
7	chr4:103998200-104007600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr4:103998200-104007600	Weak transcription	Gastric	stomach
9	chr4:103998200-104007800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr4:103998200-104008000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr4:103998200-104008000	Weak transcription	Placenta	Placenta
12	chr4:103998200-104010000	Weak transcription	Small Intestine	intestine
13	chr4:103998200-104011200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:103998200-104020400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr4:103998400-104001800	Weak transcription	Primary hematopoietic stem cells	blood
16	chr4:103998400-104001800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr4:103998400-104001800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr4:103998400-104002000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr4:103998400-104002200	Weak transcription	Fetal Stomach	stomach
20	chr4:103998400-104002400	Weak transcription	Fetal Intestine Small	intestine
21	chr4:103998400-104005400	Weak transcription	Brain Hippocampus Middle	brain
22	chr4:103998400-104005400	Weak transcription	Psoas Muscle	Psoas
23	chr4:103998400-104006400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr4:103998400-104006400	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr4:103998400-104006400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr4:103998400-104006400	Weak transcription	Brain Substantia Nigra	brain
27	chr4:103998400-104006800	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr4:103998400-104006800	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr4:103998400-104007000	Weak transcription	Right Ventricle	heart
30	chr4:103998400-104007800	Weak transcription	Pancreas	Pancrea
31	chr4:103998400-104008000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr4:103998400-104008000	Weak transcription	Colonic Mucosa	Colon
33	chr4:103998400-104008400	Weak transcription	Esophagus	oesophagus
34	chr4:103998400-104010800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr4:103998400-104018800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr4:103998600-104001000	Weak transcription	Liver	Liver
37	chr4:103998600-104001600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr4:103998600-104001800	Weak transcription	Fetal Lung	lung
39	chr4:103998600-104001800	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr4:103998600-104002000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr4:103998600-104002800	Weak transcription	Colon Smooth Muscle	Colon
42	chr4:103998600-104003000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr4:103998600-104003000	Weak transcription	Fetal Heart	heart
44	chr4:103998600-104003200	Weak transcription	HSMM	muscle
45	chr4:103998600-104005400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr4:103998600-104005600	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr4:103998600-104006400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr4:103998600-104006400	Weak transcription	GM12878-XiMat	blood
49	chr4:103998600-104006600	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr4:103998600-104006800	Weak transcription	H1 Cell Line	embryonic stem cell

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