Variant report

Variant	rs16961340
Chromosome Location	chr17:17006544-17006545
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17006139..17008392-chr17:17014164..17016773,2	K562	blood:
2	chr17:17000263..17003828-chr17:17006059..17008926,3	MCF-7	breast:
3	chr17:17006504..17008901-chr17:17010774..17012390,2	MCF-7	breast:
4	chr17:17005653..17007729-chr17:17008275..17010821,3	MCF-7	breast:
5	chr17:17001973..17004582-chr17:17006426..17009352,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12601193	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12601424	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12601453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12602196	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12602675	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes]
rs16961396	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2271521	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2292528	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3744124	1.00[CEU][hapmap]
rs3744126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3744135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3744142	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs3803762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3826304	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4078534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41319048	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4316813	0.92[JPT][hapmap]
rs4328504	0.81[ASN][1000 genomes]
rs6502557	1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs6502565	1.00[CEU][hapmap]
rs7222600	1.00[CEU][hapmap]
rs8064771	0.92[JPT][hapmap]
rs8069241	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8072214	0.87[EUR][1000 genomes]
rs8076621	0.87[EUR][1000 genomes]
rs9908728	0.84[ASN][1000 genomes]
rs9909107	0.84[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059280	chr17:16975059-17017957	Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16961340	ATP13A1	trans	brain	seeQTL
rs16961340	FLCN	cis	lymphoblastoid	seeQTL

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16986800-17013600	Weak transcription	HUVEC	blood vessel
2	chr17:16992400-17010000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr17:16993400-17011400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr17:16994600-17011600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr17:16997000-17016600	Enhancers	Left Ventricle	heart
6	chr17:16997400-17010000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr17:16998200-17016200	Enhancers	Fetal Heart	heart
8	chr17:16998600-17006800	Enhancers	Psoas Muscle	Psoas
9	chr17:16998600-17015400	Genic enhancers	Fetal Muscle Leg	muscle
10	chr17:16998600-17016600	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr17:16999000-17012800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr17:16999600-17008200	Strong transcription	Primary B cells from peripheral blood	blood
13	chr17:17000200-17012600	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr17:17000200-17018200	Weak transcription	NH-A	brain
15	chr17:17000600-17008000	Strong transcription	NHEK	skin
16	chr17:17000600-17009800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr17:17000600-17009800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr17:17001400-17007000	Weak transcription	Primary B cells from cord blood	blood
19	chr17:17001600-17010200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr17:17001600-17010800	Weak transcription	Aorta	Aorta
21	chr17:17001600-17011400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr17:17001800-17006600	Weak transcription	Primary hematopoietic stem cells	blood
23	chr17:17001800-17009200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr17:17001800-17009800	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr17:17001800-17012800	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr17:17002000-17008400	Weak transcription	Hela-S3	cervix
27	chr17:17002000-17010200	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr17:17002000-17010600	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr17:17002000-17010600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr17:17002000-17011400	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr17:17002400-17007400	Strong transcription	Muscle Satellite Cultured Cells	--
32	chr17:17002400-17011600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr17:17002600-17007400	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr17:17002600-17009400	Weak transcription	Stomach Mucosa	stomach
35	chr17:17002600-17009800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr17:17002600-17010800	Weak transcription	Brain Germinal Matrix	brain
37	chr17:17002600-17011200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr17:17002600-17011400	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr17:17002600-17012000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr17:17002600-17023200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr17:17002800-17006600	Strong transcription	Duodenum Mucosa	Duodenum
42	chr17:17002800-17006600	Weak transcription	Rectal Smooth Muscle	rectum
43	chr17:17002800-17007400	Weak transcription	Colon Smooth Muscle	Colon
44	chr17:17002800-17007400	Weak transcription	NHLF	lung
45	chr17:17002800-17008400	Weak transcription	NHDF-Ad	bronchial
46	chr17:17002800-17011600	Weak transcription	Small Intestine	intestine
47	chr17:17003000-17007600	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr17:17003000-17009600	Strong transcription	Osteobl	bone
49	chr17:17003000-17010000	Weak transcription	Fetal Kidney	kidney
50	chr17:17003000-17010800	Genic enhancers	Fetal Muscle Trunk	muscle

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