Variant report

Variant	rs2280400
Chromosome Location	chr17:38349127-38349128
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:38348399..38350901-chr17:38351389..38353492,2	MCF-7	breast:
2	chr17:38348080..38350590-chr17:38501950..38504205,2	K562	blood:
3	chr17:38330070..38334400-chr17:38346938..38351108,4	K562	blood:
4	chr17:38343845..38346711-chr17:38349005..38352130,3	K562	blood:
5	chr17:38343298..38345399-chr17:38347624..38349920,2	MCF-7	breast:
6	chr17:38334977..38338913-chr17:38347829..38351366,4	MCF-7	breast:
7	chr17:38337616..38339944-chr17:38348078..38350196,2	K562	blood:
8	chr17:38345427..38348504-chr17:38348993..38351022,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000108352	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs11078940	0.85[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap]
rs12103921	0.99[ASN][1000 genomes]
rs12944717	0.93[ASN][1000 genomes]
rs12946680	0.87[GIH][hapmap];0.83[TSI][hapmap]
rs13706	0.85[CEU][hapmap];0.87[GIH][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap]
rs16965666	0.80[CHD][hapmap];0.85[JPT][hapmap]
rs16965687	0.85[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2077464	0.87[GIH][hapmap];0.89[TSI][hapmap]
rs2120200	0.87[GIH][hapmap]
rs2314338	0.88[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs28537537	0.85[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs28663197	0.81[ASN][1000 genomes]
rs34223321	1.00[ASN][1000 genomes]
rs36030243	0.87[GIH][hapmap]
rs3744806	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4077125	0.94[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap]
rs45567834	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4566234	0.94[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap]
rs55767073	0.83[AMR][1000 genomes]
rs55772196	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55835834	0.88[ASN][1000 genomes]
rs55991953	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56013073	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56029626	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs59018914	0.88[ASN][1000 genomes]
rs59861136	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs61024420	0.91[ASN][1000 genomes]
rs6503537	0.82[ASN][1000 genomes]
rs6503539	0.94[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs67597966	0.94[ASN][1000 genomes]
rs7211770	0.83[CHD][hapmap];0.85[JPT][hapmap]
rs7217852	0.87[GIH][hapmap];0.89[TSI][hapmap]
rs72836633	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72836634	0.94[ASN][1000 genomes]
rs72836635	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs72836636	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs72836639	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs72836640	0.89[ASN][1000 genomes]
rs72836641	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs72836642	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs72836648	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7359537	0.85[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7405635	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs8066144	0.85[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap]
rs8073925	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs8082192	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9303285	0.83[TSI][hapmap]
rs9303286	0.92[CEU][hapmap]
rs9891718	0.81[ASN][1000 genomes]
rs9892404	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9892946	0.94[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap]
rs9892973	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9893520	0.85[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.81[ASN][1000 genomes]
rs9895163	0.81[ASN][1000 genomes]
rs9897092	0.81[ASN][1000 genomes]
rs9901109	0.85[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap]
rs9904021	0.94[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.89[TSI][hapmap]
rs9904270	0.85[CEU][hapmap];0.87[GIH][hapmap];0.89[TSI][hapmap]
rs9906409	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9907683	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9908034	0.88[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs9908257	0.85[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs9908354	0.97[ASN][1000 genomes]
rs9911840	0.82[ASN][1000 genomes]
rs9912082	0.83[ASN][1000 genomes]
rs9916460	0.85[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap]
rs9916782	0.85[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833444	chr17:38242823-38437280	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv525796	chr17:38306365-38405037	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38338000-38349800	Weak transcription	Dnd41	blood
2	chr17:38348000-38350200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr17:38348000-38350400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr17:38348000-38350400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr17:38348000-38350400	Weak transcription	Gastric	stomach
6	chr17:38348000-38350800	Strong transcription	Sigmoid Colon	Sigmoid Colon
7	chr17:38348000-38351000	Weak transcription	Spleen	Spleen
8	chr17:38348000-38353400	Weak transcription	Aorta	Aorta
9	chr17:38348200-38349800	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr17:38348200-38350000	Weak transcription	Lung	lung
11	chr17:38348200-38350200	Strong transcription	Colonic Mucosa	Colon
12	chr17:38348200-38350200	Strong transcription	Duodenum Mucosa	Duodenum
13	chr17:38348200-38350200	Weak transcription	HSMMtube	muscle
14	chr17:38348200-38350600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr17:38348200-38350800	Strong transcription	Rectal Mucosa Donor 31	rectum
16	chr17:38348200-38351600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr17:38348200-38351600	Weak transcription	Right Ventricle	heart
18	chr17:38348200-38353200	Weak transcription	Thymus	Thymus
19	chr17:38348400-38349200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr17:38348400-38349200	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr17:38348400-38349200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr17:38348400-38349200	Weak transcription	Brain Angular Gyrus	brain
23	chr17:38348400-38349200	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr17:38348400-38349200	Weak transcription	Left Ventricle	heart
25	chr17:38348400-38349400	Weak transcription	Brain Anterior Caudate	brain
26	chr17:38348400-38349800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr17:38348400-38349800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr17:38348400-38349800	Weak transcription	Fetal Muscle Trunk	muscle
29	chr17:38348400-38349800	Strong transcription	NHEK	skin
30	chr17:38348400-38350200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr17:38348400-38350200	Weak transcription	Stomach Mucosa	stomach
32	chr17:38348400-38350200	Weak transcription	HSMM	muscle
33	chr17:38348400-38350400	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr17:38348400-38350600	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr17:38348400-38350600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr17:38348400-38351000	Strong transcription	Fetal Intestine Small	intestine
37	chr17:38348400-38351400	Weak transcription	NH-A	brain
38	chr17:38348400-38351600	Weak transcription	NHLF	lung
39	chr17:38348400-38352000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr17:38348400-38352000	Weak transcription	Brain Cingulate Gyrus	brain
41	chr17:38348400-38352200	Weak transcription	Brain Substantia Nigra	brain
42	chr17:38348400-38354600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr17:38348400-38358200	Weak transcription	Adipose Nuclei	Adipose
44	chr17:38348400-38358400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr17:38348600-38349200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr17:38348600-38349200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr17:38348600-38349400	Strong transcription	HMEC	breast
48	chr17:38348600-38349600	Weak transcription	Brain Hippocampus Middle	brain
49	chr17:38348600-38349600	Weak transcription	K562	blood
50	chr17:38348600-38349800	Weak transcription	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links