Variant report

Variant	rs17249336
Chromosome Location	chr19:38441136-38441137
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38438618..38442193-chr19:38444314..38446890,3	MCF-7	breast:
2	chr19:38440998..38442982-chr19:38537686..38540589,2	MCF-7	breast:
3	chr19:38395717..38398405-chr19:38438245..38443084,4	MCF-7	breast:
4	chr19:38440256..38441798-chr19:38479359..38480943,2	K562	blood:

Variant related genes	Relation type
ENSG00000171804	Chromatin interaction
ENSG00000105738	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs12150862	0.81[AMR][1000 genomes]
rs12151082	0.81[AMR][1000 genomes]
rs1643455	1.00[CHB][hapmap]
rs1643459	1.00[CHB][hapmap]
rs17248670	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs17249138	0.84[AMR][1000 genomes]
rs17306900	1.00[CHB][hapmap];1.00[MEX][hapmap]
rs3859549	1.00[CHB][hapmap]
rs4536583	0.92[CEU][hapmap];1.00[CHB][hapmap]
rs55752822	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55785437	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs55813548	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55946812	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs55974157	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55983118	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55994045	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56080901	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56184201	0.84[AMR][1000 genomes]
rs56207124	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56230664	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56233644	0.83[AMR][1000 genomes]
rs56246446	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56251160	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56252444	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56300335	0.99[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs56676595	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6508755	1.00[CHB][hapmap];0.83[GIH][hapmap];0.94[MEX][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs705501	1.00[CHB][hapmap]
rs7245855	1.00[CHB][hapmap];1.00[MEX][hapmap]
rs7245962	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7257266	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7258011	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73027472	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73027480	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs73034922	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73036634	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73036658	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7343065	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8100199	1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs833905	1.00[CHB][hapmap]
rs833919	1.00[CHB][hapmap]
rs833920	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
2	nsv1061106	chr19:38400149-38448723	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv544001	chr19:38400149-38448723	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs17249336	ARHGEF1	cis	cerebellum	SCAN
rs17249336	KIAA0961	cis	multi-tissue	Pritchard
rs17249336	AC012309.5	cis	Artery Tibial	GTEx
rs17249336	C19orf61	cis	cerebellum	SCAN
rs17249336	AC012309.5	cis	Esophagus Mucosa	GTEx
rs17249336	AC012309.5	cis	Heart Left Ventricle	GTEx
rs17249336	AC012309.5	cis	Thyroid	GTEx
rs17249336	ZNF585B	cis	Esophagus Muscularis	GTEx
rs17249336	ZNF781	cis	Thyroid	GTEx
rs17249336	ZNF226	cis	cerebellum	SCAN
rs17249336	TRAPPC6A	cis	cerebellum	SCAN
rs17249336	AC012309.5	cis	Esophagus Muscularis	GTEx
rs17249336	PLEKHG2	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38399600-38441200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr19:38423200-38443000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr19:38423600-38444400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr19:38424800-38444000	Weak transcription	NHDF-Ad	bronchial
5	chr19:38425000-38454000	Weak transcription	HSMMtube	muscle
6	chr19:38426400-38444000	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr19:38426600-38442600	Weak transcription	HMEC	breast
8	chr19:38426600-38448200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr19:38426600-38450800	Weak transcription	Ovary	ovary
10	chr19:38426800-38443800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr19:38427000-38441200	Weak transcription	Adipose Nuclei	Adipose
12	chr19:38427000-38441200	Weak transcription	Left Ventricle	heart
13	chr19:38427000-38444000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr19:38427000-38444000	Weak transcription	Fetal Brain Female	brain
15	chr19:38427200-38443800	Weak transcription	NHEK	skin
16	chr19:38427200-38444200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr19:38427400-38443600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr19:38427600-38443600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr19:38428600-38443400	Weak transcription	Fetal Stomach	stomach
20	chr19:38429200-38443800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr19:38429400-38441400	Weak transcription	Primary hematopoietic stem cells	blood
22	chr19:38429800-38442600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr19:38430600-38444000	Weak transcription	HSMM	muscle
24	chr19:38430600-38453600	Weak transcription	Aorta	Aorta
25	chr19:38432400-38443200	Weak transcription	Stomach Smooth Muscle	stomach
26	chr19:38432600-38441200	Weak transcription	Esophagus	oesophagus
27	chr19:38432600-38442600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr19:38432600-38443400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr19:38432800-38443800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr19:38433000-38444000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr19:38434000-38447800	Weak transcription	Hela-S3	cervix
32	chr19:38434200-38443000	Weak transcription	Right Atrium	heart
33	chr19:38434400-38441200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr19:38434400-38444200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr19:38434400-38451800	Weak transcription	Primary T cells from cord blood	blood
36	chr19:38435200-38444000	Weak transcription	Colonic Mucosa	Colon
37	chr19:38436600-38443800	Weak transcription	Fetal Intestine Large	intestine
38	chr19:38436600-38444000	Weak transcription	Duodenum Mucosa	Duodenum
39	chr19:38437200-38441800	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr19:38438400-38455600	Enhancers	Primary B cells from peripheral blood	blood
41	chr19:38438600-38441800	Genic enhancers	GM12878-XiMat	blood
42	chr19:38438800-38441400	Weak transcription	Psoas Muscle	Psoas
43	chr19:38438800-38443400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr19:38439000-38445200	Weak transcription	Fetal Heart	heart
45	chr19:38439200-38441200	Weak transcription	Fetal Muscle Trunk	muscle
46	chr19:38439200-38441800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr19:38439400-38441800	Strong transcription	Fetal Intestine Small	intestine
48	chr19:38439400-38442600	Weak transcription	Stomach Mucosa	stomach
49	chr19:38439600-38441200	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr19:38439600-38441600	Genic enhancers	A549	lung

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