Variant report

Variant	rs1445940
Chromosome Location	chr5:52393421-52393422
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:52392231..52395065-chr5:52398498..52400912,2	K562	blood:
2	chr5:52391585..52394108-chr5:52394132..52397970,3	K562	blood:
3	chr5:52391291..52394442-chr5:52402494..52406194,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164172	Chromatin interaction
ENSG00000247796	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10051425	0.94[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10051483	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10055919	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10058715	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10065574	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10065693	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1042324	0.80[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10471829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10471830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10513009	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1139484	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13356629	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13357783	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16880872	1.00[CEU][hapmap];0.91[YRI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16880873	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16880890	0.80[YRI][hapmap]
rs16880892	0.89[CEU][hapmap]
rs1801106	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2193969	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2233214	0.91[EUR][1000 genomes]
rs2287873	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2303120	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2303125	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28841614	0.91[EUR][1000 genomes]
rs2910966	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2974984	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3021373	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212444	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3212468	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3212487	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3212491	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3212492	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212493	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212497	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3212498	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212503	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212504	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3212515	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3212523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3212526	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3212528	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3212529	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3212536	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212539	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212543	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212544	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3212545	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3212546	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212548	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212558	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3212567	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212568	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212569	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212570	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3212573	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212579	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3212580	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212582	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212584	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212585	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3212586	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3212588	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3212593	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3212606	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212607	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3212612	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212613	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3212615	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3212628	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212633	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3212634	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212635	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3212643	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3213805	1.00[CEU][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3797474	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3815755	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7446448	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs7700416	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7737412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs875657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv830296	chr5:52209528-52410253	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS 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	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52336400-52399800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr5:52341200-52396400	Strong transcription	HMEC	breast
3	chr5:52341400-52396400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:52347800-52395000	Weak transcription	Psoas Muscle	Psoas
5	chr5:52348600-52394800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr5:52356800-52394000	Weak transcription	Fetal Kidney	kidney
7	chr5:52365800-52394800	Weak transcription	Right Ventricle	heart
8	chr5:52370400-52394600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr5:52370400-52404600	Weak transcription	Brain Germinal Matrix	brain
10	chr5:52372000-52394800	Weak transcription	Colonic Mucosa	Colon
11	chr5:52372000-52394800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr5:52372200-52394800	Weak transcription	Gastric	stomach
13	chr5:52372200-52394800	Weak transcription	Pancreas	Pancrea
14	chr5:52372400-52404400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr5:52378400-52405000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr5:52381200-52394200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr5:52382800-52395000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr5:52383000-52394800	Weak transcription	Brain Anterior Caudate	brain
19	chr5:52383200-52394800	Weak transcription	Esophagus	oesophagus
20	chr5:52383200-52394800	Weak transcription	Spleen	Spleen
21	chr5:52383800-52395000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr5:52384000-52394600	Weak transcription	Brain Angular Gyrus	brain
23	chr5:52384000-52394800	Weak transcription	Brain Substantia Nigra	brain
24	chr5:52384000-52395200	Weak transcription	Brain Hippocampus Middle	brain
25	chr5:52384200-52394800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr5:52385800-52394000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr5:52385800-52394600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr5:52385800-52395800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr5:52386200-52394800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr5:52386400-52394800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr5:52386400-52394800	Weak transcription	GM12878-XiMat	blood
32	chr5:52386600-52394800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr5:52387400-52394800	Weak transcription	Fetal Brain Male	brain
34	chr5:52387600-52394800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr5:52387600-52405000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr5:52388000-52394000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr5:52388000-52394200	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr5:52388000-52394800	Weak transcription	Ovary	ovary
39	chr5:52388000-52395000	Weak transcription	Lung	lung
40	chr5:52388200-52394200	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr5:52388200-52398400	Strong transcription	HUVEC	blood vessel
42	chr5:52388400-52396200	Weak transcription	Hela-S3	cervix
43	chr5:52389400-52404800	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr5:52389600-52395000	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr5:52389800-52394800	Weak transcription	Primary hematopoietic stem cells	blood
46	chr5:52390000-52397600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr5:52390200-52403800	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr5:52390600-52394200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr5:52390600-52394600	Weak transcription	Fetal Thymus	thymus
50	chr5:52390600-52396200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links