Variant report

Variant	rs11557453
Chromosome Location	chr3:141333835-141333836
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:141204106..141207979-chr3:141333280..141335871,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RASA2-1	chr3:141331749-141334185	NONHSAT092438

Variant related genes	Relation type
ENSG00000155903	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11707656	0.86[EUR][1000 genomes]
rs11711318	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11713714	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11714208	1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11717144	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11717842	0.84[CEU][hapmap]
rs12695740	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12695741	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12695743	0.88[CEU][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13062809	0.93[ASN][1000 genomes]
rs13067519	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13068454	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13072100	0.84[CEU][hapmap]
rs13078872	0.84[CEU][hapmap]
rs13083593	0.84[CEU][hapmap]
rs13084444	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs13088429	0.84[CEU][hapmap]
rs13095168	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13099945	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2312194	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2312266	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34317570	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34342794	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3732872	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3806647	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4334619	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6769161	1.00[JPT][hapmap]
rs71619392	0.80[EUR][1000 genomes]
rs720663	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7624941	1.00[JPT][hapmap]
rs7649666	1.00[JPT][hapmap]
rs7651511	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9289629	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs9289634	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9808953	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9822575	0.88[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9823528	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9829588	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830055	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9833121	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9836050	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9836818	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9837202	0.81[CEU][hapmap]
rs9838230	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9838419	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9840159	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9840697	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9843866	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9849180	0.84[CEU][hapmap];0.81[AMR][1000 genomes]
rs9850416	0.88[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9851256	1.00[CHB][hapmap]
rs9865971	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9868956	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9870749	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9873042	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141265200-141336200	Weak transcription	Psoas Muscle	Psoas
2	chr3:141277200-141341400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:141313200-141344000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:141320400-141337200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr3:141321800-141342600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:141324200-141336000	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr3:141324800-141334000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:141325000-141338000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:141325600-141335000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:141326600-141334000	Strong transcription	Dnd41	blood
11	chr3:141326600-141334200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:141326600-141335400	Strong transcription	HUVEC	blood vessel
13	chr3:141326800-141334000	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr3:141326800-141335600	Strong transcription	Primary B cells from cord blood	blood
15	chr3:141328800-141336000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr3:141330000-141338800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:141330200-141336600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr3:141330200-141338200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr3:141330400-141334400	Weak transcription	Fetal Muscle Leg	muscle
20	chr3:141330400-141334600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:141330400-141334600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr3:141330400-141334800	Weak transcription	NH-A	brain
23	chr3:141330400-141335600	Weak transcription	Hela-S3	cervix
24	chr3:141330400-141336400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr3:141330400-141336400	Weak transcription	NHEK	skin
26	chr3:141330400-141337000	Weak transcription	Lung	lung
27	chr3:141330400-141337400	Weak transcription	HSMMtube	muscle
28	chr3:141330400-141337800	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr3:141330400-141338000	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr3:141330400-141342000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr3:141330400-141342000	Weak transcription	Pancreas	Pancrea
32	chr3:141330400-141343200	Weak transcription	Brain Angular Gyrus	brain
33	chr3:141330400-141344000	Weak transcription	HMEC	breast
34	chr3:141330400-141344600	Weak transcription	NHLF	lung
35	chr3:141330600-141334600	Weak transcription	Fetal Stomach	stomach
36	chr3:141330600-141335200	Weak transcription	Spleen	Spleen
37	chr3:141330600-141336400	Weak transcription	Fetal Intestine Small	intestine
38	chr3:141330600-141336800	Weak transcription	Thymus	Thymus
39	chr3:141330600-141337600	Weak transcription	Brain Germinal Matrix	brain
40	chr3:141330600-141338000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr3:141330600-141338200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:141330600-141339000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr3:141330600-141339200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr3:141330600-141344200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr3:141330600-141344200	Weak transcription	Ovary	ovary
46	chr3:141330800-141336000	Weak transcription	Fetal Intestine Large	intestine
47	chr3:141330800-141338400	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr3:141330800-141338400	Weak transcription	Left Ventricle	heart
49	chr3:141330800-141344200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr3:141331600-141338800	Weak transcription	HUES48 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links