Variant report

Variant	rs12601422
Chromosome Location	chr17:16943623-16943624
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:16943176..16945630-chr17:17102978..17105800,2	K562	blood:
2	chr17:16930112..16931615-chr17:16942008..16944719,2	K562	blood:
3	chr17:16941343..16943728-chr17:16947873..16949492,2	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1047799	0.88[CHB][hapmap];0.83[CHD][hapmap]
rs10852844	0.81[ASN][1000 genomes]
rs11078368	0.83[ASN][1000 genomes]
rs11078371	0.94[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs11078372	0.81[ASN][1000 genomes]
rs11078373	0.94[CHB][hapmap];0.83[CHD][hapmap]
rs11651938	0.94[CHB][hapmap]
rs11652678	0.93[CHB][hapmap]
rs11654887	0.94[CHB][hapmap]
rs11657189	0.94[CHB][hapmap]
rs11658904	0.87[MEX][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs11870422	0.85[ASN][1000 genomes]
rs11870997	0.85[ASN][1000 genomes]
rs12451343	0.81[ASN][1000 genomes]
rs12602592	0.94[CHB][hapmap]
rs12602839	0.83[ASN][1000 genomes]
rs12603417	0.83[ASN][1000 genomes]
rs1567815	0.94[CHB][hapmap]
rs17794784	0.88[CHB][hapmap]
rs2292526	0.94[CHB][hapmap]
rs2292530	0.88[CHB][hapmap];0.83[CHD][hapmap]
rs28452405	0.81[ASN][1000 genomes]
rs34001712	0.81[ASN][1000 genomes]
rs35650871	0.84[ASN][1000 genomes]
rs3744125	0.94[CHB][hapmap]
rs3744131	0.88[CHB][hapmap]
rs3744132	0.94[CHB][hapmap];0.83[CHD][hapmap]
rs3744134	0.88[CHB][hapmap];0.81[CHD][hapmap]
rs3744136	0.94[CHB][hapmap]
rs3744137	0.88[CHB][hapmap];0.83[CHD][hapmap]
rs3744138	0.88[CHB][hapmap];0.83[CHD][hapmap]
rs3744139	0.88[CHB][hapmap];0.83[CHD][hapmap]
rs4073688	0.82[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap]
rs4074612	0.94[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs4589617	0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4629023	0.94[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs4641803	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4985703	0.94[CHB][hapmap]
rs4985704	0.88[CHB][hapmap];0.83[CHD][hapmap]
rs4985716	0.86[ASN][1000 genomes]
rs4985721	0.81[ASN][1000 genomes]
rs4985728	0.83[ASN][1000 genomes]
rs4985737	0.94[CHB][hapmap]
rs4985741	0.88[CHB][hapmap];0.83[CHD][hapmap]
rs4985742	0.94[CHB][hapmap];0.83[CHD][hapmap]
rs57729820	0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs60128647	0.83[ASN][1000 genomes]
rs61242604	0.87[ASN][1000 genomes]
rs7212275	0.86[ASN][1000 genomes]
rs7214429	0.88[CHB][hapmap];0.83[CHD][hapmap]
rs7218781	0.94[CHB][hapmap];0.83[CHD][hapmap]
rs7223686	0.91[MEX][hapmap];0.82[AMR][1000 genomes]
rs73979060	0.83[ASN][1000 genomes]
rs73979078	0.83[ASN][1000 genomes]
rs8066234	0.88[CHB][hapmap];0.83[CHD][hapmap]
rs8071254	0.87[ASN][1000 genomes]
rs8076273	0.94[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9892695	0.91[ASN][1000 genomes]
rs9906028	0.84[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	nsv1058863	chr17:16812121-16943780	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv543227	chr17:16812121-16943780	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv543231	chr17:16926227-16950644	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12601422	C17orf39	cis	cerebellum	SCAN
rs12601422	FLCN	cis	cerebellum	SCAN
rs12601422	M-RIP	Cis_1M	lymphoblastoid	RTeQTL
rs12601422	RANBP9	trans	parietal	SCAN
rs12601422	ALDH3A2	cis	parietal	SCAN
rs12601422	LOC162632	cis	parietal	SCAN
rs12601422	MPRIP	cis	lymphoblastoid	seeQTL

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16932800-16944200	Weak transcription	Fetal Brain Female	brain
2	chr17:16934600-16944600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr17:16935600-16944400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr17:16935800-16945200	Weak transcription	Aorta	Aorta
5	chr17:16936000-16944200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr17:16936000-16944400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr17:16936000-16944400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr17:16936000-16944400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr17:16936000-16944400	Weak transcription	Colonic Mucosa	Colon
10	chr17:16936000-16944400	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr17:16936000-16944400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr17:16936000-16944400	Enhancers	A549	lung
13	chr17:16936000-16944400	Weak transcription	NHEK	skin
14	chr17:16936000-16944600	Weak transcription	Gastric	stomach
15	chr17:16936000-16944600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr17:16936000-16944800	Weak transcription	Brain Angular Gyrus	brain
17	chr17:16936000-16944800	Weak transcription	Esophagus	oesophagus
18	chr17:16936200-16944200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr17:16936200-16944400	Weak transcription	Brain Substantia Nigra	brain
20	chr17:16936200-16944400	Weak transcription	Colon Smooth Muscle	Colon
21	chr17:16936200-16944400	Weak transcription	Stomach Mucosa	stomach
22	chr17:16936200-16944800	Weak transcription	HUVEC	blood vessel
23	chr17:16937400-16944400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr17:16939200-16944600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr17:16939600-16944400	Weak transcription	K562	blood
26	chr17:16940400-16944200	Weak transcription	Stomach Smooth Muscle	stomach
27	chr17:16940400-16944400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr17:16940400-16944400	Weak transcription	Brain Hippocampus Middle	brain
29	chr17:16940400-16944400	Weak transcription	Fetal Heart	heart
30	chr17:16940400-16944400	Weak transcription	Fetal Thymus	thymus
31	chr17:16940400-16944400	Weak transcription	Right Ventricle	heart
32	chr17:16940400-16944600	Weak transcription	Left Ventricle	heart
33	chr17:16940400-16944600	Weak transcription	NH-A	brain
34	chr17:16940400-16944800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr17:16940400-16944800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr17:16940400-16944800	Weak transcription	Right Atrium	heart
37	chr17:16940600-16944200	Weak transcription	HSMM	muscle
38	chr17:16940600-16944200	Weak transcription	NHLF	lung
39	chr17:16940600-16944800	Weak transcription	Primary B cells from cord blood	blood
40	chr17:16940600-16944800	Weak transcription	Primary B cells from peripheral blood	blood
41	chr17:16940600-16945000	Weak transcription	Primary hematopoietic stem cells	blood
42	chr17:16940800-16944600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr17:16941000-16944400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr17:16941000-16944400	Weak transcription	Fetal Lung	lung
45	chr17:16941000-16944400	Weak transcription	Osteobl	bone
46	chr17:16941200-16944200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr17:16941200-16944200	Weak transcription	Placenta	Placenta
48	chr17:16941200-16944200	Weak transcription	NHDF-Ad	bronchial
49	chr17:16941200-16944400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr17:16941200-16944400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links