Variant report

Variant	rs338598
Chromosome Location	chr19:41701528-41701529
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:41700366..41702638-chr19:41769140..41770960,2	MCF-7	breast:
2	chr19:41700466..41703429-chr19:41707889..41710444,2	K562	blood:
3	chr19:41700112..41702823-chr19:41703297..41705172,2	MCF-7	breast:
4	chr19:41698985..41702051-chr19:41767021..41770015,3	MCF-7	breast:
5	chr19:41698406..41703429-chr19:41707121..41711829,4	K562	blood:
6	chr19:41700678..41702956-chr19:41802683..41805056,2	K562	blood:
7	chr19:41695919..41698717-chr19:41700424..41702047,2	K562	blood:

Variant related genes	Relation type
ENSG00000264423	Chromatin interaction
ENSG00000105323	Chromatin interaction
ENSG00000167600	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1628289	0.84[CHD][hapmap]
rs1709138	0.83[MEX][hapmap]
rs338593	0.82[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.89[ASN][1000 genomes]
rs338594	0.85[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]

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	nsv911767	chr19:41649516-41716271	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv523521	chr19:41680424-41702426	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv911768	chr19:41680424-41748753	Flanking Bivalent TSS/Enh Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs338598	HRC	cis	parietal	SCAN
rs338598	MARK4	cis	parietal	SCAN
rs338598	CADM4	cis	cerebellum	SCAN
rs338598	PSG9	cis	parietal	SCAN
rs338598	QPCTL	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41699600-41724400	Weak transcription	Right Atrium	heart
2	chr19:41699800-41702000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr19:41699800-41702000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr19:41700000-41722200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr19:41700000-41724400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr19:41700200-41701600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr19:41700200-41701800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr19:41700200-41724200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:41700400-41701600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr19:41700400-41701600	Enhancers	HepG2	liver
11	chr19:41700400-41701800	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
12	chr19:41700400-41702000	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
13	chr19:41700600-41701600	Weak transcription	NHLF	lung
14	chr19:41700600-41701800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr19:41700600-41702000	Weak transcription	Esophagus	oesophagus
16	chr19:41700600-41702200	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr19:41700600-41702600	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr19:41700600-41702600	Enhancers	A549	lung
19	chr19:41700600-41702800	Genic enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr19:41700600-41703000	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr19:41700600-41704000	Weak transcription	Colonic Mucosa	Colon
22	chr19:41700600-41707000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr19:41700600-41714600	Weak transcription	Spleen	Spleen
24	chr19:41700800-41701600	Genic enhancers	Fetal Intestine Small	intestine
25	chr19:41700800-41701800	Genic enhancers	HUES6 Cell Line	embryonic stem cell
26	chr19:41700800-41701800	Enhancers	Rectal Mucosa Donor 29	rectum
27	chr19:41700800-41702000	Weak transcription	Gastric	stomach
28	chr19:41700800-41702200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr19:41700800-41703000	Genic enhancers	H1 Cell Line	embryonic stem cell
30	chr19:41700800-41703000	Enhancers	Monocytes-CD14+_RO01746	blood
31	chr19:41700800-41703200	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr19:41700800-41704200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr19:41700800-41704600	Weak transcription	Lung	lung
34	chr19:41700800-41705200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr19:41700800-41711400	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr19:41701200-41701600	Genic enhancers	H9 Cell Line	embryonic stem cell
37	chr19:41701200-41701800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr19:41701200-41702000	Genic enhancers	HUES64 Cell Line	embryonic stem cell
39	chr19:41701200-41702000	Enhancers	Duodenum Mucosa	Duodenum
40	chr19:41701200-41702200	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
41	chr19:41701200-41702400	Enhancers	HMEC	breast
42	chr19:41701200-41704800	Strong transcription	Fetal Intestine Large	intestine
43	chr19:41701200-41713800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr19:41701400-41701600	Flanking Active TSS	NHEK	skin
45	chr19:41701400-41702600	Enhancers	GM12878-XiMat	blood
46	chr19:41701400-41703000	Genic enhancers	Stomach Mucosa	stomach

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