Variant report

Variant	rs6554088
Chromosome Location	chr4:54173860-54173861
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10002674	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10010450	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10032378	0.82[YRI][hapmap]
rs11133259	0.87[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs12507175	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13137917	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13141050	0.91[AFR][1000 genomes]
rs13146978	0.84[AFR][1000 genomes]
rs13148823	0.86[AFR][1000 genomes]
rs13150432	0.89[YRI][hapmap]
rs1471596	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2128104	1.00[YRI][hapmap]
rs2412396	0.85[AFR][1000 genomes]
rs2412408	0.82[AFR][1000 genomes]
rs3910858	1.00[MKK][hapmap]
rs4552533	0.84[AFR][1000 genomes]
rs4864447	1.00[MKK][hapmap]
rs4864448	0.82[AFR][1000 genomes]
rs4864449	0.87[AFR][1000 genomes]
rs4864462	0.80[YRI][hapmap];1.00[AMR][1000 genomes]
rs4864738	0.84[AFR][1000 genomes]
rs4864764	0.82[YRI][hapmap]
rs6554066	1.00[MKK][hapmap]
rs6554067	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs6554076	0.86[AFR][1000 genomes]
rs6554085	0.91[AFR][1000 genomes]
rs6554097	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6554101	1.00[AMR][1000 genomes]
rs6821777	0.82[YRI][hapmap];1.00[AMR][1000 genomes]
rs6823086	1.00[AMR][1000 genomes]
rs6825367	0.89[AFR][1000 genomes]
rs6832823	0.86[AFR][1000 genomes]
rs6834711	0.89[MKK][hapmap]
rs6847795	1.00[AMR][1000 genomes]
rs6850629	1.00[AMR][1000 genomes]
rs6855673	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs7656204	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs7663263	0.86[AFR][1000 genomes]
rs7680828	0.86[AFR][1000 genomes]
rs7687290	0.82[YRI][hapmap]
rs7693858	0.89[AFR][1000 genomes]
rs7697807	0.82[YRI][hapmap]
rs900113	1.00[YRI][hapmap]
rs9684941	0.82[YRI][hapmap];1.00[AMR][1000 genomes]

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	nsv1008593	chr4:54120297-54207769	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54140200-54179000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:54164400-54177400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr4:54168200-54188000	Weak transcription	Left Ventricle	heart
4	chr4:54169200-54180000	Weak transcription	Brain Hippocampus Middle	brain
5	chr4:54169200-54187800	Weak transcription	Liver	Liver
6	chr4:54169400-54178600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr4:54169400-54187400	Weak transcription	Dnd41	blood
8	chr4:54169600-54187800	Weak transcription	Brain Angular Gyrus	brain
9	chr4:54169800-54181400	Weak transcription	Fetal Lung	lung
10	chr4:54169800-54181400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr4:54169800-54187800	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr4:54169800-54216200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr4:54170000-54181400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr4:54170000-54183800	Weak transcription	Primary B cells from peripheral blood	blood
15	chr4:54170000-54186800	Weak transcription	HSMM	muscle
16	chr4:54170600-54187600	Weak transcription	K562	blood
17	chr4:54170600-54230600	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr4:54170800-54174000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr4:54170800-54174000	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr4:54170800-54181400	Weak transcription	Fetal Thymus	thymus
21	chr4:54171200-54179200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr4:54171200-54188000	Weak transcription	Esophagus	oesophagus
23	chr4:54171600-54181200	Weak transcription	Duodenum Mucosa	Duodenum
24	chr4:54171600-54181400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr4:54171600-54181400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr4:54171600-54187600	Weak transcription	Primary monocytes fromperipheralblood	blood
27	chr4:54171800-54177600	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr4:54171800-54181400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr4:54172000-54176400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr4:54172000-54181200	Weak transcription	Fetal Intestine Small	intestine
31	chr4:54172000-54188000	Weak transcription	Pancreas	Pancrea
32	chr4:54172000-54188000	Weak transcription	HepG2	liver
33	chr4:54172200-54174200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr4:54172200-54174600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr4:54172200-54180800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr4:54172200-54181800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr4:54172400-54174200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr4:54172400-54174200	Strong transcription	Primary T cells from cord blood	blood
39	chr4:54172400-54174600	Weak transcription	Ovary	ovary
40	chr4:54172400-54175600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr4:54172600-54215400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr4:54172800-54174200	Enhancers	NHLF	lung
43	chr4:54172800-54174400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr4:54172800-54174600	Strong transcription	Primary B cells from cord blood	blood
45	chr4:54173000-54174200	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr4:54173000-54174200	Strong transcription	A549	lung
47	chr4:54173000-54174800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr4:54173000-54187600	Weak transcription	Brain Anterior Caudate	brain
49	chr4:54173200-54174200	Flanking Active TSS	NHDF-Ad	bronchial
50	chr4:54173200-54177800	Weak transcription	Gastric	stomach

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