Variant report

Variant	rs16909865
Chromosome Location	chr9:98207302-98207303
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:98197509..98199344-chr9:98205458..98207531,2	MCF-7	breast:
2	chr9:98206913..98208735-chr9:98254383..98256847,2	MCF-7	breast:
3	chr9:98195671..98199206-chr9:98203414..98207469,4	K562	blood:
4	chr9:98202595..98206584-chr9:98206995..98209232,3	MCF-7	breast:
5	chr9:98200946..98203462-chr9:98205677..98208531,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C9orf3-6	chr9:98207060-98208373	NONHSAT133370

Variant related genes	Relation type
ENSG00000185920	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10512249	0.85[CHB][hapmap]
rs16909856	0.91[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs16909859	0.91[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs16909898	0.85[CHB][hapmap]
rs16909902	0.85[CHB][hapmap]
rs2282040	0.85[CHB][hapmap]
rs2282043	0.81[CEU][hapmap]
rs28421389	0.86[EUR][1000 genomes]
rs28485160	0.87[EUR][1000 genomes]
rs28517704	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs28563972	0.84[EUR][1000 genomes]
rs28615951	0.89[EUR][1000 genomes]
rs357530	1.00[AFR][1000 genomes]
rs357531	1.00[AFR][1000 genomes]
rs357535	1.00[AFR][1000 genomes]
rs357541	1.00[AFR][1000 genomes]
rs357545	1.00[AFR][1000 genomes]
rs357555	1.00[AFR][1000 genomes]
rs357560	1.00[AFR][1000 genomes]
rs357561	1.00[AFR][1000 genomes]
rs3824488	0.81[CEU][hapmap];0.85[CHB][hapmap]
rs419574	1.00[ASW][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];1.00[AFR][1000 genomes]
rs57247461	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs58831996	0.88[EUR][1000 genomes]
rs60608001	0.89[EUR][1000 genomes]
rs61652825	0.87[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	nsv531633	chr9:98078300-98431120	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv831658	chr9:98152971-98342178	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv949520	chr9:98204199-98238358	Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv430083	chr9:98204245-98445645	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16909865	PTCH1	cis	lymphoblastoid	seeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98189600-98210800	Weak transcription	Right Atrium	heart
2	chr9:98197200-98207600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr9:98197200-98208800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr9:98197800-98209400	Weak transcription	Fetal Heart	heart
5	chr9:98198000-98207400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr9:98200800-98211800	Weak transcription	Fetal Brain Male	brain
7	chr9:98202000-98224600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr9:98202800-98207800	Weak transcription	Hela-S3	cervix
9	chr9:98203200-98207600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr9:98203200-98208800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr9:98203400-98208600	Weak transcription	Colonic Mucosa	Colon
12	chr9:98203600-98207600	Weak transcription	Brain Angular Gyrus	brain
13	chr9:98203600-98211200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr9:98204400-98208400	Weak transcription	Spleen	Spleen
15	chr9:98204400-98209600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr9:98204400-98220400	Strong transcription	Fetal Intestine Large	intestine
17	chr9:98204600-98209000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr9:98204600-98209800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr9:98204600-98212800	Strong transcription	Fetal Lung	lung
20	chr9:98204600-98214400	Weak transcription	Osteobl	bone
21	chr9:98204800-98224400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr9:98205000-98209600	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr9:98205000-98210000	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr9:98205200-98207600	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr9:98205200-98209000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr9:98205200-98218000	Weak transcription	Small Intestine	intestine
27	chr9:98205400-98208400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr9:98205400-98208800	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr9:98205600-98207400	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr9:98205600-98207400	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr9:98205600-98207600	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr9:98205600-98207600	Weak transcription	A549	lung
33	chr9:98205600-98208600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr9:98205600-98212600	Weak transcription	Colon Smooth Muscle	Colon
35	chr9:98205800-98207600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr9:98206000-98210800	Weak transcription	K562	blood
37	chr9:98206000-98216000	Weak transcription	Primary T cells from cord blood	blood
38	chr9:98206000-98224400	Weak transcription	HUVEC	blood vessel
39	chr9:98206000-98237600	Weak transcription	Psoas Muscle	Psoas
40	chr9:98206200-98208000	Strong transcription	Fetal Stomach	stomach
41	chr9:98206200-98221400	Strong transcription	Fetal Intestine Small	intestine
42	chr9:98206400-98210200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr9:98206400-98217600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr9:98206400-98218400	Weak transcription	NHEK	skin
45	chr9:98206600-98208400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr9:98206600-98209600	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr9:98206600-98209600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr9:98206600-98209600	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr9:98206600-98209600	Strong transcription	Stomach Smooth Muscle	stomach
50	chr9:98206600-98209800	Strong transcription	HUES6 Cell Line	embryonic stem cell

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