Variant report

Variant	rs17852635
Chromosome Location	chr19:18186575-18186576
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:18185308..18187156-chr19:18263394..18266366,3	MCF-7	breast:
2	chr19:18185895..18188337-chr19:18214059..18216560,2	K562	blood:
3	chr19:18175848..18177697-chr19:18184239..18186730,2	MCF-7	breast:
4	chr19:18184421..18186715-chr19:18208443..18210278,2	K562	blood:
5	chr19:18183643..18186690-chr19:18187876..18191058,3	K562	blood:
6	chr19:18179477..18182800-chr19:18183743..18186734,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105647	Chromatin interaction
ENSG00000096996	Chromatin interaction
ENSG00000099308	Chromatin interaction
ENSG00000268173	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11575934	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17879486	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17886247	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17887036	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2644777	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs365179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs366653	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs372889	0.81[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs373654	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs375947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs376008	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3761041	0.82[CHB][hapmap]
rs381607	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs382634	0.89[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs383483	0.88[ASN][1000 genomes]
rs391410	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs401502	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs404733	0.82[JPT][hapmap]
rs429774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs452265	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs453263	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs455034	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62121127	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7255688	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055932	chr19:17923918-18369944	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv543923	chr19:17923918-18369944	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
3	nsv532614	chr19:18033043-18573963	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	204 gene(s)	inside rSNPs	diseases
4	nsv470130	chr19:18047283-18234587	Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
5	esv1837595	chr19:18085428-18393682	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	147 gene(s)	inside rSNPs	diseases
6	nsv833773	chr19:18152971-18302988	Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv911237	chr19:18169449-18193060	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
8	nsv911239	chr19:18173603-18191059	Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17852635	KLHL26	cis	cerebellum	SCAN
rs17852635	OR7A5	cis	cerebellum	SCAN
rs17852635	CYP4F8	cis	cerebellum	SCAN
rs17852635	PALM3	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18169200-18190000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr19:18169600-18195000	Weak transcription	Gastric	stomach
3	chr19:18170200-18197000	Weak transcription	Primary B cells from cord blood	blood
4	chr19:18179600-18194200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr19:18181400-18191400	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr19:18182600-18197600	Weak transcription	Right Atrium	heart
7	chr19:18182800-18187200	Strong transcription	Spleen	Spleen
8	chr19:18184400-18188200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr19:18184400-18191400	Weak transcription	Thymus	Thymus
10	chr19:18184400-18197400	Weak transcription	Lung	lung
11	chr19:18184600-18187400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
12	chr19:18184600-18188800	Strong transcription	Primary T cells from cord blood	blood
13	chr19:18184600-18194200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr19:18184600-18194200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr19:18184800-18190200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr19:18185000-18188200	Weak transcription	Primary B cells from peripheral blood	blood
17	chr19:18185000-18189000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr19:18185000-18197400	Weak transcription	Colonic Mucosa	Colon
19	chr19:18185200-18186600	Weak transcription	GM12878-XiMat	blood
20	chr19:18185200-18186600	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr19:18185200-18194200	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr19:18185400-18186600	Weak transcription	Fetal Thymus	thymus
23	chr19:18185400-18194800	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr19:18186200-18187400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr19:18186400-18186800	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr19:18186400-18187200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr19:18186400-18187200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
28	chr19:18186400-18187200	Strong transcription	Duodenum Mucosa	Duodenum
29	chr19:18186400-18187400	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr19:18186400-18189800	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr19:18186400-18194400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links