Variant report

Variant	rs4985741
Chromosome Location	chr17:17087880-17087881
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr17:17087387-17088192	U87	brain:	n/a	n/a
2	POLR2A	chr17:17087333-17088085	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:17086210..17088657-chr17:17181524..17183953,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C17orf84-1	chr17:17087243-17091977	predAs_engstrom06_CD171782_1

Variant related genes	Relation type
MPRIP	TF binding region

Extended variants
information (count: 67 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs1047799	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1047805	0.98[ASN][1000 genomes]
rs10852844	0.80[ASN][1000 genomes]
rs10852846	0.91[ASN][1000 genomes]
rs11078371	0.94[CHB][hapmap];1.00[CHD][hapmap]
rs11078372	0.80[ASN][1000 genomes]
rs11078373	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1110505	0.94[ASN][1000 genomes]
rs11551189	0.94[ASN][1000 genomes]
rs11651938	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11652678	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11654887	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11657189	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11870035	0.92[ASN][1000 genomes]
rs11870483	0.83[ASN][1000 genomes]
rs12601422	0.88[CHB][hapmap];0.83[CHD][hapmap]
rs12602583	0.98[ASN][1000 genomes]
rs12602592	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1567815	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17794784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2292526	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2292530	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2349645	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2349648	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28452405	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34001712	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34976658	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3744125	0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3744127	0.98[ASN][1000 genomes]
rs3744131	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3744132	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3744134	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3744136	0.94[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs3744137	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.92[ASN][1000 genomes]
rs3744138	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.92[ASN][1000 genomes]
rs3744139	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3826305	0.97[ASN][1000 genomes]
rs4073688	0.83[CHB][hapmap];0.97[CHD][hapmap]
rs4074612	0.94[CHB][hapmap]
rs4074819	0.90[ASN][1000 genomes]
rs4283273	0.98[ASN][1000 genomes]
rs4321246	0.90[ASN][1000 genomes]
rs4629023	0.94[CHB][hapmap];1.00[CHD][hapmap]
rs4985703	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4985704	0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4985721	0.81[ASN][1000 genomes]
rs4985730	0.83[ASN][1000 genomes]
rs4985737	0.94[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs4985742	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4985743	0.97[ASN][1000 genomes]
rs4985745	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56133536	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58326998	0.91[ASN][1000 genomes]
rs59394251	0.91[ASN][1000 genomes]
rs7211576	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7214429	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[YRI][hapmap];0.94[ASN][1000 genomes]
rs7216677	0.90[ASN][1000 genomes]
rs7218781	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs8066111	0.86[ASN][1000 genomes]
rs8066234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8069259	0.89[ASN][1000 genomes]
rs8077360	0.90[ASN][1000 genomes]
rs9893676	0.94[ASN][1000 genomes]
rs9895060	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9897510	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9910857	0.86[EUR][1000 genomes];0.92[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	nsv907728	chr17:17013189-17095487	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4985741	ZNF624	cis	parietal	SCAN
rs4985741	TOM1L2	cis	cerebellum	SCAN
rs4985741	FLCN	cis	cerebellum	SCAN
rs4985741	FLCN	cis	parietal	SCAN
rs4985741	M-RIP	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17029800-17088400	Strong transcription	Dnd41	blood
2	chr17:17030000-17088000	Strong transcription	Duodenum Mucosa	Duodenum
3	chr17:17030400-17089200	Strong transcription	Fetal Intestine Large	intestine
4	chr17:17038400-17093800	Strong transcription	Fetal Brain Female	brain
5	chr17:17045000-17088400	Strong transcription	Brain Germinal Matrix	brain
6	chr17:17045200-17093800	Strong transcription	Fetal Stomach	stomach
7	chr17:17051000-17093200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr17:17053200-17088200	Strong transcription	Gastric	stomach
9	chr17:17055200-17089400	Strong transcription	Rectal Mucosa Donor 31	rectum
10	chr17:17055600-17092600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr17:17055800-17092600	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr17:17056000-17093600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
13	chr17:17056200-17088200	Strong transcription	Duodenum Smooth Muscle	Duodenum
14	chr17:17056200-17092400	Strong transcription	Stomach Smooth Muscle	stomach
15	chr17:17056600-17093600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr17:17056800-17095000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr17:17059400-17089000	Strong transcription	A549	lung
18	chr17:17060400-17088200	Strong transcription	HSMM	muscle
19	chr17:17060400-17093400	Strong transcription	Liver	Liver
20	chr17:17060600-17088800	Strong transcription	Fetal Intestine Small	intestine
21	chr17:17060600-17089200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr17:17060800-17089000	Strong transcription	NHLF	lung
23	chr17:17060800-17089400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr17:17060800-17093600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr17:17061400-17089000	Strong transcription	Osteobl	bone
26	chr17:17061400-17090200	Strong transcription	Muscle Satellite Cultured Cells	--
27	chr17:17067800-17092200	Strong transcription	Brain Cingulate Gyrus	brain
28	chr17:17073800-17088000	Strong transcription	NHDF-Ad	bronchial
29	chr17:17074000-17088200	Strong transcription	Pancreas	Pancrea
30	chr17:17074000-17088400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr17:17075200-17088200	Strong transcription	Ovary	ovary
32	chr17:17075200-17089000	Strong transcription	Brain Angular Gyrus	brain
33	chr17:17076000-17088000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr17:17076000-17088600	Strong transcription	NHEK	skin
35	chr17:17076200-17089000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr17:17076200-17092600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr17:17076200-17094600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr17:17076400-17088000	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr17:17076400-17088200	Strong transcription	Brain Hippocampus Middle	brain
40	chr17:17076600-17104600	Weak transcription	K562	blood
41	chr17:17080800-17090800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr17:17082800-17088000	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
43	chr17:17082800-17089600	Genic enhancers	Primary B cells from peripheral blood	blood
44	chr17:17082800-17091000	Genic enhancers	Fetal Thymus	thymus
45	chr17:17083000-17088000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
46	chr17:17083000-17088400	Genic enhancers	Left Ventricle	heart
47	chr17:17083200-17088000	Strong transcription	HepG2	liver
48	chr17:17083200-17088200	Strong transcription	Rectal Smooth Muscle	rectum
49	chr17:17083400-17090800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr17:17083600-17093200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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