Variant report

Variant	rs2412740
Chromosome Location	chr15:43009448-43009449
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:43004420..43008133-chr15:43008696..43011545,3	K562	blood:
2	chr15:43007694..43010580-chr15:43015984..43019053,4	K562	blood:
3	chr15:43007397..43009798-chr15:43011681..43013458,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140326	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10162939	0.82[EUR][1000 genomes]
rs10400824	0.85[EUR][1000 genomes]
rs1197548	0.82[EUR][1000 genomes]
rs1197549	0.82[EUR][1000 genomes]
rs1197550	0.82[EUR][1000 genomes]
rs1197551	0.82[EUR][1000 genomes]
rs12102055	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12594483	1.00[AFR][1000 genomes]
rs12594855	0.96[AFR][1000 genomes]
rs12903762	0.81[EUR][1000 genomes]
rs12905592	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12906497	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12907826	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12912064	0.93[EUR][1000 genomes]
rs12917018	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12917189	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs16957020	0.86[EUR][1000 genomes]
rs16957091	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16957104	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1705356	0.82[EUR][1000 genomes]
rs1915241	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1995939	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2136900	0.93[EUR][1000 genomes]
rs2136901	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2280048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2305084	0.89[EUR][1000 genomes]
rs2412741	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28479391	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28549876	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28562951	0.92[EUR][1000 genomes]
rs28744617	0.81[EUR][1000 genomes]
rs28798437	0.85[EUR][1000 genomes]
rs28811114	0.84[EUR][1000 genomes]
rs28823029	0.84[EUR][1000 genomes]
rs3099758	0.82[EUR][1000 genomes]
rs3199486	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34191150	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35616173	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35738819	0.96[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs3742987	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3742988	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4265781	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4923950	0.96[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs4924690	0.96[AFR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4924691	0.86[EUR][1000 genomes]
rs58938096	0.81[EUR][1000 genomes]
rs623271	0.82[EUR][1000 genomes]
rs6493059	0.86[EUR][1000 genomes]
rs6493060	0.90[ASN][1000 genomes]
rs6493061	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6493062	0.82[AMR][1000 genomes]
rs6493063	0.89[EUR][1000 genomes]
rs6493066	0.82[EUR][1000 genomes]
rs67391479	0.91[EUR][1000 genomes]
rs7163030	0.90[EUR][1000 genomes]
rs7166373	0.96[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7166775	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7167392	0.88[EUR][1000 genomes]
rs7169009	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7169202	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7174041	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7175582	0.92[EUR][1000 genomes]
rs7182141	0.89[EUR][1000 genomes]
rs7182479	0.83[EUR][1000 genomes]
rs7183487	0.81[EUR][1000 genomes]
rs731984	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8026233	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8027427	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8030587	0.95[ASN][1000 genomes]
rs8034447	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8034664	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8043472	0.96[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9269	0.94[EUR][1000 genomes]
rs9783713	0.92[EUR][1000 genomes]
rs9919994	0.94[EUR][1000 genomes]
rs9920163	0.84[EUR][1000 genomes]
rs9944248	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528725	chr15:42755555-43104406	Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv427959	chr15:42931181-43207353	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS 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	10 gene(s)	inside rSNPs	diseases
3	nsv457122	chr15:42948862-43062548	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv569238	chr15:42948862-43062548	Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv517553	chr15:42970899-43023482	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42908800-43015000	Weak transcription	Fetal Kidney	kidney
2	chr15:42975600-43011400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr15:42976600-43015200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:42977000-43011600	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr15:42977000-43016600	Weak transcription	Hela-S3	cervix
6	chr15:42978200-43010400	Weak transcription	Thymus	Thymus
7	chr15:42978800-43012000	Weak transcription	NH-A	brain
8	chr15:42979200-43011000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr15:42979600-43010000	Weak transcription	GM12878-XiMat	blood
10	chr15:42979800-43010600	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr15:42980400-43010400	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr15:42981400-43015000	Weak transcription	HSMM	muscle
13	chr15:42981600-43009800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr15:42981600-43011000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr15:42981800-43010000	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr15:42984000-43014800	Weak transcription	K562	blood
17	chr15:42986000-43018400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr15:42987200-43010000	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr15:42987800-43016400	Weak transcription	Esophagus	oesophagus
20	chr15:42988000-43010200	Weak transcription	Colonic Mucosa	Colon
21	chr15:42988200-43010200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr15:42988400-43009600	Weak transcription	Fetal Intestine Small	intestine
23	chr15:42988400-43010600	Weak transcription	NHLF	lung
24	chr15:42989000-43010000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr15:42989000-43010400	Weak transcription	Placenta	Placenta
26	chr15:42989000-43011800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr15:42989200-43009600	Weak transcription	Left Ventricle	heart
28	chr15:42989200-43010200	Weak transcription	Brain Angular Gyrus	brain
29	chr15:42989200-43010200	Weak transcription	Ovary	ovary
30	chr15:42993400-43010200	Weak transcription	Primary T cells from cord blood	blood
31	chr15:42993400-43010800	Weak transcription	Fetal Lung	lung
32	chr15:42993400-43015400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr15:42994200-43010000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr15:42997200-43011000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr15:42997200-43016400	Weak transcription	Pancreas	Pancrea
36	chr15:42999800-43011800	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr15:43000600-43011400	Weak transcription	NHEK	skin
38	chr15:43000800-43018600	Weak transcription	A549	lung
39	chr15:43001000-43014800	Weak transcription	HUVEC	blood vessel
40	chr15:43001400-43009800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr15:43003200-43011200	Weak transcription	Fetal Heart	heart
42	chr15:43003200-43011600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr15:43003200-43012000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr15:43003400-43011000	Weak transcription	Primary T cells fromperipheralblood	blood
45	chr15:43004200-43016200	Weak transcription	Psoas Muscle	Psoas
46	chr15:43004800-43010200	Weak transcription	Gastric	stomach
47	chr15:43005800-43010200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr15:43006400-43011800	Weak transcription	Primary B cells from peripheral blood	blood
49	chr15:43007000-43011400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr15:43007200-43026800	Strong transcription	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links