Variant report

Variant	rs10913915
Chromosome Location	chr1:179925855-179925856
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:179925797-179925925	K562	blood:	n/a	n/a
2	MYC	chr1:179925768-179926656	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:179844528..179853403-chr1:179920065..179927793,25	K562	blood:
2	chr1:179845348..179847730-chr1:179923811..179926342,3	MCF-7	breast:
3	chr1:179892500..179895461-chr1:179925642..179927756,2	K562	blood:
4	chr1:179921069..179927710-chr1:179937007..179944258,10	K562	blood:
5	chr1:179924257..179926025-chr1:179973260..179975368,2	K562	blood:
6	chr1:179849016..179853452-chr1:179922333..179928502,16	K562	blood:
7	chr1:179847679..179853408-chr1:179922379..179926886,15	MCF-7	breast:
8	chr1:179923952..179925915-chr1:180137472..180139404,2	MCF-7	breast:
9	chr1:179921415..179925789-chr1:179925828..179929752,13	MCF-7	breast:
10	chr1:179884565..179886596-chr1:179924353..179925912,2	MCF-7	breast:
11	chr1:179909218..179916721-chr1:179922197..179926382,9	K562	blood:
12	chr1:179924119..179925876-chr1:179942859..179944489,2	MCF-7	breast:
13	chr1:179923898..179926923-chr1:180121889..180124249,4	MCF-7	breast:
14	chr1:179923938..179925991-chr1:180198274..180200305,2	MCF-7	breast:
15	chr1:179842979..179846933-chr1:179922588..179926684,5	K562	blood:
16	chr1:179924485..179926237-chr20:44016912..44018546,2	MCF-7	breast:
17	chr1:179848142..179854405-chr1:179919774..179927189,17	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000260360	TF binding region
ENSG00000116260	Chromatin interaction
ENSG00000235145	Chromatin interaction
ENSG00000232880	Chromatin interaction
ENSG00000135837	Chromatin interaction
ENSG00000169905	Chromatin interaction
ENSG00000143337	Chromatin interaction
ENSG00000272906	Chromatin interaction
ENSG00000261831	Chromatin interaction
ENSG00000260360	Chromatin interaction
ENSG00000121454	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10798731	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs10798733	1.00[ASN][1000 genomes]
rs10913911	1.00[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913912	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913913	1.00[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913921	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913922	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913926	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];1.00[ASN][1000 genomes]
rs10913928	1.00[ASN][1000 genomes]
rs10913929	1.00[ASN][1000 genomes]
rs11579402	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];1.00[ASN][1000 genomes]
rs11589421	1.00[CHB][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12117957	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12119113	1.00[ASN][1000 genomes]
rs12120822	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124175	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124336	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12127248	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12129928	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12131995	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12135952	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12136838	1.00[CHB][hapmap]
rs12137562	1.00[CHB][hapmap]
rs12138251	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12141545	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12144757	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12743903	1.00[ASN][1000 genomes]
rs12744192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs3845390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4083553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4652477	1.00[ASN][1000 genomes]
rs4652478	1.00[ASN][1000 genomes]
rs55676403	1.00[ASN][1000 genomes]
rs55882713	1.00[ASN][1000 genomes]
rs56166206	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58121876	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59953116	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61605706	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6425605	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6693288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6702845	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs72710619	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72710658	1.00[ASN][1000 genomes]
rs7521701	1.00[ASN][1000 genomes]
rs7521873	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7522347	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7533903	1.00[ASN][1000 genomes]
rs7538086	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7539784	1.00[ASN][1000 genomes]
rs7550093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7555418	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs9425484	1.00[CEU][hapmap]
rs9425862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9425864	1.00[ASN][1000 genomes]
rs9425869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv1815608	chr1:179813499-180067988	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers ZNF genes & repeats 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	48 gene(s)	inside rSNPs	diseases
3	nsv429958	chr1:179814306-179994628	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179922600-179926000	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr1:179922800-179926000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr1:179922800-179926000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:179922800-179926000	Active TSS	Psoas Muscle	Psoas
5	chr1:179922800-179926800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:179922800-179926800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:179922800-179927000	Active TSS	Fetal Intestine Large	intestine
8	chr1:179923000-179926000	Active TSS	Ovary	ovary
9	chr1:179923200-179926200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr1:179923200-179926200	Active TSS	Muscle Satellite Cultured Cells	--
11	chr1:179923200-179926600	Active TSS	NHLF	lung
12	chr1:179923600-179926600	Active TSS	HMEC	breast
13	chr1:179923600-179926600	Active TSS	K562	blood
14	chr1:179923600-179928000	Active TSS	GM12878-XiMat	blood
15	chr1:179924600-179926000	Active TSS	Right Atrium	heart
16	chr1:179924600-179926400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:179924800-179926200	Active TSS	HepG2	liver
18	chr1:179924800-179926400	Active TSS	Skeletal Muscle Female	skeletal muscle
19	chr1:179924800-179927000	Flanking Active TSS	Dnd41	blood
20	chr1:179924800-179935600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr1:179924800-179937800	Weak transcription	Spleen	Spleen
22	chr1:179924800-179938000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:179924800-179938000	Weak transcription	Lung	lung
24	chr1:179924800-179963600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:179925000-179926600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:179925000-179926800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr1:179925200-179926000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr1:179925200-179926000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
29	chr1:179925200-179926800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:179925200-179927000	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr1:179925200-179927600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr1:179925200-179928200	Weak transcription	Left Ventricle	heart
33	chr1:179925200-179946200	Weak transcription	Stomach Mucosa	stomach
34	chr1:179925400-179926000	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr1:179925400-179926000	Enhancers	Colon Smooth Muscle	Colon
36	chr1:179925400-179926000	Enhancers	Rectal Smooth Muscle	rectum
37	chr1:179925400-179926400	Enhancers	Brain Angular Gyrus	brain
38	chr1:179925400-179927000	Enhancers	Primary neutrophils fromperipheralblood	blood
39	chr1:179925400-179927000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr1:179925400-179927200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr1:179925400-179927600	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr1:179925400-179927800	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr1:179925400-179927800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr1:179925400-179928400	Enhancers	Primary T killer memory cells from peripheral blood	blood
45	chr1:179925400-179929800	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr1:179925400-179931000	Weak transcription	Fetal Thymus	thymus
47	chr1:179925400-179946000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr1:179925600-179926000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:179925600-179926000	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr1:179925600-179926000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links