Variant report

Variant	rs28541279
Chromosome Location	chr4:110398890-110398891
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	chr4:110396923..110399404-chr4:110400868..110402670,2	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10003981	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10005225	1.00[EUR][1000 genomes]
rs10008457	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10009463	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10011971	1.00[EUR][1000 genomes]
rs10016533	0.94[LWK][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes]
rs10020652	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10030694	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17040433	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17040466	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17040486	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs17040498	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17040565	1.00[CEU][hapmap]
rs28412073	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28460762	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28595287	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28597954	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28663368	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28680423	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28723468	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28829974	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57705376	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6533431	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6533432	1.00[CEU][hapmap];0.96[YRI][hapmap];1.00[EUR][1000 genomes]
rs6812917	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6830772	1.00[MEX][hapmap];1.00[TSI][hapmap]
rs6834714	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6837083	1.00[EUR][1000 genomes]
rs6838597	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6840561	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6852062	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6854516	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72898791	1.00[EUR][1000 genomes]
rs7665738	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7667502	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7674196	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7677736	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7681265	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7685647	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7697001	1.00[CEU][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9997563	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];1.00[EUR][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	nsv461613	chr4:109922064-110593460	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv595129	chr4:109922064-110593460	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3349784	chr4:110348873-110723163	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv525385	chr4:110395146-110466413	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110378800-110415800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr4:110384800-110399800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr4:110384800-110401000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr4:110385400-110402800	Weak transcription	Brain Germinal Matrix	brain
5	chr4:110385400-110403000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr4:110385600-110415800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr4:110385600-110415800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr4:110385600-110415800	Weak transcription	Esophagus	oesophagus
9	chr4:110385800-110415600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr4:110385800-110415800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr4:110385800-110415800	Weak transcription	Colonic Mucosa	Colon
12	chr4:110386000-110415800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr4:110386200-110415800	Weak transcription	Lung	lung
14	chr4:110386200-110415800	Weak transcription	Spleen	Spleen
15	chr4:110386400-110413600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr4:110386400-110415600	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr4:110386400-110415800	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr4:110386600-110402400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr4:110386600-110415600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr4:110386800-110402400	Weak transcription	Fetal Lung	lung
21	chr4:110386800-110405200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr4:110386800-110415600	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr4:110387000-110402200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr4:110387000-110402200	Weak transcription	Fetal Muscle Trunk	muscle
25	chr4:110387000-110402800	Weak transcription	Brain Angular Gyrus	brain
26	chr4:110387000-110415600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr4:110387000-110415800	Weak transcription	Fetal Brain Male	brain
28	chr4:110387000-110415800	Weak transcription	Fetal Brain Female	brain
29	chr4:110387000-110416400	Weak transcription	Right Ventricle	heart
30	chr4:110387200-110415600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr4:110387600-110415600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr4:110388000-110403600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr4:110389400-110402200	Weak transcription	Primary hematopoietic stem cells	blood
34	chr4:110390000-110415400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr4:110391600-110402000	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr4:110391800-110415400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr4:110391800-110415600	Weak transcription	Ovary	ovary
38	chr4:110393000-110415600	Weak transcription	Fetal Stomach	stomach
39	chr4:110393000-110415600	Weak transcription	Thymus	Thymus
40	chr4:110393000-110415800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr4:110393000-110415800	Weak transcription	Gastric	stomach
42	chr4:110393000-110415800	Weak transcription	Left Ventricle	heart
43	chr4:110393000-110415800	Weak transcription	Pancreas	Pancrea
44	chr4:110393000-110417400	Weak transcription	Psoas Muscle	Psoas
45	chr4:110393200-110403000	Weak transcription	Placenta	Placenta
46	chr4:110393200-110405000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr4:110393200-110412400	Weak transcription	Fetal Muscle Leg	muscle
48	chr4:110393200-110415600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr4:110393200-110415800	Weak transcription	Small Intestine	intestine
50	chr4:110393200-110422600	Weak transcription	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links