Variant report

Variant	rs6043924
Chromosome Location	chr20:16381626-16381627
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12479724	0.82[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap]
rs12480677	0.85[CEU][hapmap];0.95[CHB][hapmap]
rs1884660	0.91[MEX][hapmap];0.81[TSI][hapmap]
rs2144944	0.81[CHD][hapmap];0.90[JPT][hapmap]
rs3746783	0.80[CHD][hapmap];0.95[JPT][hapmap]
rs41276372	0.88[ASN][1000 genomes]
rs4814483	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4814489	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6034469	0.81[CEU][hapmap];0.95[TSI][hapmap];0.80[EUR][1000 genomes]
rs6043938	0.81[JPT][hapmap]
rs6111071	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs6111090	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6111113	0.91[MEX][hapmap];0.81[TSI][hapmap]
rs6131818	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs761901	0.91[MEX][hapmap];0.81[TSI][hapmap]

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	nsv833931	chr20:16308276-16460596	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6043924	HSPC072	cis	parietal	SCAN
rs6043924	ISM1	cis	parietal	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:16316000-16384400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr20:16343600-16384600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr20:16345000-16391200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr20:16345400-16391000	Weak transcription	Brain Germinal Matrix	brain
5	chr20:16346600-16393600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr20:16347600-16392000	Weak transcription	Fetal Kidney	kidney
7	chr20:16348400-16383600	Weak transcription	Small Intestine	intestine
8	chr20:16350000-16384000	Weak transcription	HepG2	liver
9	chr20:16350000-16384200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr20:16350800-16384200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr20:16353000-16384200	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr20:16355400-16385200	Weak transcription	Brain Substantia Nigra	brain
13	chr20:16356000-16384200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr20:16357200-16383600	Weak transcription	Brain Anterior Caudate	brain
15	chr20:16357800-16385400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr20:16359800-16387800	Weak transcription	Placenta	Placenta
17	chr20:16360600-16382400	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr20:16360600-16385200	Weak transcription	Primary hematopoietic stem cells	blood
19	chr20:16360800-16385000	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr20:16360800-16385200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr20:16364600-16385400	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr20:16366400-16391400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr20:16367200-16387800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr20:16372200-16389400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr20:16372400-16389200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr20:16372600-16383600	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr20:16372600-16388200	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr20:16372600-16404600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr20:16372800-16384200	Weak transcription	Esophagus	oesophagus
30	chr20:16372800-16385400	Weak transcription	Spleen	Spleen
31	chr20:16373200-16384400	Weak transcription	NHEK	skin
32	chr20:16373400-16384200	Weak transcription	Colonic Mucosa	Colon
33	chr20:16374200-16382600	Weak transcription	Primary B cells from peripheral blood	blood
34	chr20:16375400-16392600	Weak transcription	NH-A	brain
35	chr20:16375400-16396400	Weak transcription	Stomach Mucosa	stomach
36	chr20:16377000-16382600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr20:16377000-16383000	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr20:16377000-16384400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr20:16377000-16389400	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr20:16378000-16384600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr20:16378000-16385400	Weak transcription	Pancreas	Pancrea
42	chr20:16378000-16388000	Weak transcription	HSMM	muscle
43	chr20:16378000-16388200	Weak transcription	Osteobl	bone
44	chr20:16378000-16391200	Weak transcription	Brain Cingulate Gyrus	brain
45	chr20:16378000-16404400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr20:16378200-16384400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr20:16378200-16385600	Weak transcription	Brain Angular Gyrus	brain
48	chr20:16378600-16385600	Weak transcription	Colon Smooth Muscle	Colon
49	chr20:16378600-16388400	Weak transcription	Fetal Brain Female	brain
50	chr20:16378600-16391200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links