Variant report

Variant	rs17839544
Chromosome Location	chr16:30491783-30491784
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:30490143..30492856-chr16:30536156..30538564,2	MCF-7	breast:
2	chr16:30491445..30493060-chr16:30498871..30500808,2	K562	blood:

Variant related genes	Relation type
ENSG00000005844	Chromatin interaction
ENSG00000169957	Chromatin interaction
ENSG00000261346	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10871452	0.94[CEU][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs11862597	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs17790906	1.00[GIH][hapmap]
rs2230434	1.00[ASW][hapmap];1.00[GIH][hapmap]
rs35069260	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs55919902	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs67575585	0.90[EUR][1000 genomes]
rs7195241	0.88[EUR][1000 genomes]
rs9934579	0.93[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.96[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	nsv532531	chr16:30370550-30581820	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	113 gene(s)	inside rSNPs	diseases
2	nsv1062456	chr16:30442166-31253997	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
3	nsv542898	chr16:30442166-31253997	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	437 gene(s)	inside rSNPs	diseases
4	nsv1783	chr16:30449450-30494321	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17839544	RP11-347C12.2	cis	Stomach	GTEx
rs17839544	BCL7C	cis	cerebellum	SCAN
rs17839544	PRR14	cis	parietal	SCAN
rs17839544	SEZ6L2	cis	Cerebellum	GTEx
rs17839544	CLN3	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30485200-30499600	Weak transcription	Liver	Liver
2	chr16:30485600-30500200	Weak transcription	Dnd41	blood
3	chr16:30485800-30492800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr16:30485800-30500200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr16:30485800-30521400	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr16:30486000-30510600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr16:30486200-30494600	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr16:30486800-30494800	Weak transcription	Lung	lung
9	chr16:30486800-30495600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr16:30486800-30533400	Weak transcription	Esophagus	oesophagus
11	chr16:30487000-30494000	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr16:30487000-30494600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr16:30487000-30497000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
14	chr16:30487000-30497000	Weak transcription	Fetal Intestine Small	intestine
15	chr16:30487000-30534800	Strong transcription	Primary neutrophils fromperipheralblood	blood
16	chr16:30487400-30502000	Genic enhancers	Primary T cells fromperipheralblood	blood
17	chr16:30487600-30500000	Weak transcription	Placenta	Placenta
18	chr16:30488200-30495800	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr16:30488400-30492000	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr16:30488600-30496200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr16:30489000-30505400	Weak transcription	Duodenum Mucosa	Duodenum
22	chr16:30489000-30534000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr16:30489800-30496000	Strong transcription	Primary T cells from cord blood	blood
24	chr16:30490000-30494400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
25	chr16:30490000-30494400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
26	chr16:30490000-30518800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr16:30490200-30492200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr16:30490200-30493000	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr16:30490200-30497600	Strong transcription	Primary B cells from cord blood	blood
30	chr16:30490400-30495800	Strong transcription	Spleen	Spleen
31	chr16:30490600-30495800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr16:30490600-30521000	Weak transcription	Colonic Mucosa	Colon
33	chr16:30490800-30534600	Strong transcription	Thymus	Thymus
34	chr16:30491000-30491800	Weak transcription	GM12878-XiMat	blood
35	chr16:30491000-30492200	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr16:30491000-30513600	Strong transcription	Primary B cells from peripheral blood	blood
37	chr16:30491000-30534000	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr16:30491400-30492200	Genic enhancers	Fetal Thymus	thymus
39	chr16:30491600-30492000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr16:30491600-30511200	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr16:30491600-30533800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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