Variant report

Variant	rs1531149
Chromosome Location	chr2:173493886-173493887
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	chr2:173492299..173494515-chr2:173498149..173499767,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PDK1-1	chr2:173492557-173494290	NONHSAT075516

Extended variants
information (count: 75 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1010752	0.94[ASN][1000 genomes]
rs10930561	0.84[ASN][1000 genomes]
rs10930563	0.86[ASN][1000 genomes]
rs10930566	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10930567	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10930568	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12052531	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12464110	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12465512	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12465795	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12469378	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12476204	0.81[ASN][1000 genomes]
rs12617037	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12617921	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12618078	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12618132	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12620518	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12621044	0.95[EUR][1000 genomes]
rs12693008	0.82[ASN][1000 genomes]
rs13015260	0.81[ASN][1000 genomes]
rs1530864	0.88[ASN][1000 genomes]
rs1530865	0.88[ASN][1000 genomes]
rs1531148	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1531150	0.85[ASN][1000 genomes]
rs16860693	0.88[ASN][1000 genomes]
rs16860737	0.81[ASN][1000 genomes]
rs16860741	0.82[ASN][1000 genomes]
rs16860781	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16860789	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1869923	0.83[ASN][1000 genomes]
rs2122833	1.00[EUR][1000 genomes]
rs2599260	0.83[ASN][1000 genomes]
rs2599261	0.83[ASN][1000 genomes]
rs2599262	0.83[ASN][1000 genomes]
rs2599263	0.83[ASN][1000 genomes]
rs2599264	0.83[ASN][1000 genomes]
rs2599265	0.83[ASN][1000 genomes]
rs2599266	0.83[ASN][1000 genomes]
rs2606062	0.83[ASN][1000 genomes]
rs2606063	0.83[ASN][1000 genomes]
rs2606064	0.82[ASN][1000 genomes]
rs2606065	0.83[ASN][1000 genomes]
rs2606066	0.83[ASN][1000 genomes]
rs2606067	0.83[ASN][1000 genomes]
rs2606070	0.83[ASN][1000 genomes]
rs28761282	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35892983	0.83[ASN][1000 genomes]
rs59578456	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59685886	1.00[AFR][1000 genomes]
rs60127617	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61121406	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61505737	0.88[ASN][1000 genomes]
rs6709144	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6718681	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6719140	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6733671	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6733679	0.83[ASN][1000 genomes]
rs70937083	0.88[ASN][1000 genomes]
rs70937084	0.88[ASN][1000 genomes]
rs8179584	0.84[ASN][1000 genomes]
rs836590	0.83[ASN][1000 genomes]
rs836628	0.96[ASN][1000 genomes]
rs836629	0.83[ASN][1000 genomes]
rs836630	0.83[ASN][1000 genomes]
rs836631	0.83[ASN][1000 genomes]
rs836634	0.83[ASN][1000 genomes]
rs836643	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	esv2760591	chr2:173396905-173719520	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv875415	chr2:173444462-173501069	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv875416	chr2:173444462-173504674	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv583665	chr2:173460640-173643087	Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv875417	chr2:173460803-173501069	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv875418	chr2:173460803-173504674	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	esv2762962	chr2:173493078-173527311	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173461400-173504200	Weak transcription	NHEK	skin
2	chr2:173462200-173507400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr2:173465600-173495200	Weak transcription	Ovary	ovary
4	chr2:173471800-173495600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr2:173472600-173504600	Weak transcription	Adipose Nuclei	Adipose
6	chr2:173474600-173504400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:173478800-173496800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr2:173479600-173495800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr2:173479600-173496200	Weak transcription	Thymus	Thymus
10	chr2:173479800-173494600	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr2:173479800-173496000	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr2:173480000-173494200	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr2:173480000-173495000	Weak transcription	Primary B cells from peripheral blood	blood
14	chr2:173480000-173495200	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr2:173480000-173496000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr2:173480200-173495800	Weak transcription	GM12878-XiMat	blood
17	chr2:173480200-173499200	Weak transcription	HepG2	liver
18	chr2:173485800-173497200	Weak transcription	Brain Hippocampus Middle	brain
19	chr2:173488800-173494200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:173489200-173496200	Weak transcription	Fetal Thymus	thymus
21	chr2:173489200-173507200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr2:173489400-173494400	Weak transcription	Fetal Muscle Leg	muscle
23	chr2:173489400-173500400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr2:173489400-173504200	Weak transcription	NHLF	lung
25	chr2:173490200-173500600	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr2:173490400-173497200	Weak transcription	HSMM	muscle
27	chr2:173491400-173494800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:173491800-173494600	Strong transcription	Primary T cells from cord blood	blood
29	chr2:173491800-173494800	Strong transcription	Primary B cells from cord blood	blood
30	chr2:173491800-173494800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:173492000-173494200	Weak transcription	Aorta	Aorta
32	chr2:173492000-173494800	Strong transcription	Dnd41	blood
33	chr2:173492200-173494800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr2:173492400-173494000	Weak transcription	Pancreas	Pancrea
35	chr2:173492800-173494000	Weak transcription	Fetal Brain Male	brain
36	chr2:173492800-173494600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:173492800-173494600	Strong transcription	Fetal Stomach	stomach
38	chr2:173492800-173497600	Weak transcription	Fetal Brain Female	brain
39	chr2:173493000-173494600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr2:173493600-173494200	Weak transcription	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links