Variant report

Variant	rs16850924
Chromosome Location	chr3:140675583-140675584
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:140659457..140662013-chr3:140675174..140679419,5	K562	blood:

Variant related genes	Relation type
ENSG00000114120	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1047330	1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs1056126	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1056127	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];0.98[ASN][1000 genomes]
rs10935413	0.86[ASN][1000 genomes]
rs10935414	1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs1109282	0.86[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1109283	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11707116	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11710204	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11710926	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.93[MKK][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11711131	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];0.99[ASN][1000 genomes]
rs11713505	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11713816	1.00[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs11714438	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];0.99[ASN][1000 genomes]
rs11715248	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];0.99[ASN][1000 genomes]
rs11717097	1.00[CEU][hapmap];0.93[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11717620	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];0.99[ASN][1000 genomes]
rs11718040	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11718539	1.00[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs11718563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11720342	0.86[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12489397	1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs13063450	0.85[ASN][1000 genomes]
rs13099706	0.85[ASN][1000 genomes]
rs1568337	1.00[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs1593624	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16850915	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16850917	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16850921	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16850926	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];0.99[ASN][1000 genomes]
rs2081662	0.85[ASN][1000 genomes]
rs2292919	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2311491	0.83[ASN][1000 genomes]
rs2555702	1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs2555707	1.00[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs2871615	0.85[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.88[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35140461	0.88[ASN][1000 genomes]
rs3755764	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];0.99[ASN][1000 genomes]
rs3755765	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3773835	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3773837	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3773838	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];0.99[ASN][1000 genomes]
rs4380393	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4524250	0.87[ASN][1000 genomes]
rs4528914	0.83[ASN][1000 genomes]
rs4538351	0.84[ASN][1000 genomes]
rs57151068	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57526660	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57799705	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59128309	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59221985	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61052022	0.92[EUR][1000 genomes]
rs61151473	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61629363	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61708145	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6439962	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6439964	0.85[ASN][1000 genomes]
rs6764740	0.83[ASN][1000 genomes]
rs6770562	0.82[ASN][1000 genomes]
rs6772634	0.85[ASN][1000 genomes]
rs6773249	0.85[ASN][1000 genomes]
rs6785007	0.88[ASN][1000 genomes]
rs6785892	0.85[ASN][1000 genomes]
rs6788711	0.85[ASN][1000 genomes]
rs6789045	0.82[ASN][1000 genomes]
rs6789116	0.83[ASN][1000 genomes]
rs6797079	0.85[ASN][1000 genomes]
rs6810200	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs713354	0.81[JPT][hapmap]
rs72991025	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72991046	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7621150	1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs7626525	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7632043	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7637899	0.85[CEU][hapmap]
rs7638206	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7643287	0.94[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs7643434	1.00[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs7643614	1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs7644725	1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs7649116	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7652381	0.81[JPT][hapmap]
rs7653157	0.87[TSI][hapmap]
rs765990	0.85[ASN][1000 genomes]
rs877142	1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs957093	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591865	chr3:140396022-140728850	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1005522	chr3:140454632-140685915	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv536732	chr3:140454632-140685915	Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	esv1793115	chr3:140663107-140693053	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16850924	SLC25A36	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:140661800-140697200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:140662200-140676800	Weak transcription	Fetal Muscle Trunk	muscle
3	chr3:140662200-140696800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:140662400-140677000	Weak transcription	Fetal Thymus	thymus
5	chr3:140662400-140679000	Weak transcription	Fetal Muscle Leg	muscle
6	chr3:140662400-140692200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr3:140662600-140696800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr3:140662800-140677200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:140662800-140679200	Weak transcription	HSMMtube	muscle
10	chr3:140662800-140682200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr3:140662800-140695800	Weak transcription	NHLF	lung
12	chr3:140663000-140681600	Weak transcription	NH-A	brain
13	chr3:140663200-140676400	Weak transcription	Primary B cells from peripheral blood	blood
14	chr3:140663200-140692600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr3:140663200-140696000	Weak transcription	Fetal Stomach	stomach
16	chr3:140663400-140697400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr3:140663600-140679200	Weak transcription	Brain Cingulate Gyrus	brain
18	chr3:140663600-140692600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr3:140664000-140676600	Weak transcription	Primary T cells from cord blood	blood
20	chr3:140664000-140679000	Weak transcription	Stomach Smooth Muscle	stomach
21	chr3:140664200-140676000	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr3:140664200-140679000	Weak transcription	Primary B cells from cord blood	blood
23	chr3:140664200-140692400	Weak transcription	Fetal Brain Female	brain
24	chr3:140664200-140703800	Weak transcription	Aorta	Aorta
25	chr3:140664400-140679000	Weak transcription	Primary hematopoietic stem cells	blood
26	chr3:140664600-140677000	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr3:140664600-140677200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr3:140665400-140698400	Weak transcription	Brain Germinal Matrix	brain
29	chr3:140665800-140697600	Weak transcription	Gastric	stomach
30	chr3:140667800-140677400	Enhancers	HepG2	liver
31	chr3:140668600-140675800	Weak transcription	NHEK	skin
32	chr3:140669800-140677000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr3:140669800-140679200	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr3:140669800-140679400	Weak transcription	Brain Angular Gyrus	brain
35	chr3:140670000-140678600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr3:140670000-140679000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr3:140670000-140679000	Weak transcription	Adipose Nuclei	Adipose
38	chr3:140670000-140679200	Weak transcription	Brain Substantia Nigra	brain
39	chr3:140670000-140692600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr3:140670000-140693800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:140670000-140697200	Weak transcription	Esophagus	oesophagus
42	chr3:140670200-140679200	Weak transcription	Dnd41	blood
43	chr3:140670600-140677000	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr3:140670600-140680600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr3:140670600-140698200	Weak transcription	Spleen	Spleen
46	chr3:140670800-140696800	Weak transcription	Lung	lung
47	chr3:140671200-140676000	Weak transcription	Stomach Mucosa	stomach
48	chr3:140671200-140679600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr3:140671400-140694000	Weak transcription	Ovary	ovary
50	chr3:140671600-140679000	Weak transcription	H1 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links