Variant report

Variant	rs28480505
Chromosome Location	chr19:42883964-42883965
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	chr19:42882253..42884746-chr19:42889914..42891793,2	MCF-7	breast:
2	chr19:42876139..42879164-chr19:42881326..42883970,3	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10401235	0.84[ASN][1000 genomes]
rs10408368	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10410185	0.82[MEX][hapmap]
rs11879826	1.00[ASN][1000 genomes]
rs11880014	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11882625	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1206009	0.84[MEX][hapmap]
rs1206027	0.87[CHD][hapmap];0.82[MEX][hapmap]
rs1206028	0.84[MEX][hapmap]
rs1206029	0.87[CHD][hapmap]
rs1206033	0.87[CHD][hapmap]
rs1206038	0.87[CHD][hapmap];0.84[MEX][hapmap]
rs1206041	0.87[CHD][hapmap];0.84[MEX][hapmap]
rs12165114	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13345314	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13346080	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13346092	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13347104	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1613100	0.87[CHD][hapmap];0.84[MEX][hapmap]
rs1654623	0.87[CHD][hapmap];0.84[MEX][hapmap]
rs1676211	0.87[CHD][hapmap];0.84[MEX][hapmap]
rs1676217	0.84[MEX][hapmap]
rs2304210	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28412914	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28621009	0.87[CHD][hapmap]
rs3810147	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7257910	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73556315	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8104272	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8108964	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs851296	0.87[CHD][hapmap];0.84[MEX][hapmap]
rs9636121	0.84[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv911782	chr19:42514712-42931004	Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	nsv526186	chr19:42676481-43203507	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
5	esv2422471	chr19:42733141-43669485	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
6	nsv911785	chr19:42741124-42917545	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42830800-42884200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr19:42869000-42884400	Weak transcription	Colonic Mucosa	Colon
3	chr19:42869600-42890800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr19:42871400-42890800	Weak transcription	Psoas Muscle	Psoas
5	chr19:42872000-42884800	Weak transcription	A549	lung
6	chr19:42874400-42891000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr19:42874800-42884400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr19:42875800-42886000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr19:42876000-42884000	Weak transcription	Brain Substantia Nigra	brain
10	chr19:42877200-42890800	Weak transcription	Primary B cells from cord blood	blood
11	chr19:42877200-42890800	Weak transcription	Primary B cells from peripheral blood	blood
12	chr19:42879400-42885600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr19:42879400-42891000	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr19:42879600-42884200	Weak transcription	Dnd41	blood
15	chr19:42879600-42890800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr19:42879800-42884200	Weak transcription	Duodenum Mucosa	Duodenum
17	chr19:42879800-42884400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr19:42880000-42885200	Weak transcription	Left Ventricle	heart
19	chr19:42880000-42891000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr19:42880400-42884600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr19:42880400-42885000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr19:42880400-42885600	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr19:42880400-42891000	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr19:42880800-42884000	Weak transcription	Aorta	Aorta
25	chr19:42880800-42886000	Weak transcription	Spleen	Spleen
26	chr19:42880800-42890600	Weak transcription	Right Ventricle	heart
27	chr19:42881200-42884200	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr19:42881200-42886200	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr19:42881200-42891000	Weak transcription	Gastric	stomach
30	chr19:42881400-42884000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr19:42881400-42884200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr19:42881400-42884200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr19:42881400-42885800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr19:42881400-42891000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr19:42881400-42891000	Weak transcription	Brain Anterior Caudate	brain
36	chr19:42881400-42891200	Weak transcription	Brain Hippocampus Middle	brain
37	chr19:42881600-42884400	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr19:42881600-42891000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr19:42882000-42886200	Enhancers	Fetal Intestine Large	intestine
40	chr19:42882800-42890800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr19:42883400-42884400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr19:42883400-42884800	Weak transcription	GM12878-XiMat	blood
43	chr19:42883800-42884200	Weak transcription	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links