Variant report

Variant	rs11658904
Chromosome Location	chr17:16944622-16944623
allele	C/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	MAZ	chr17:16944269-16946136	IMR90	lung:	n/a	n/a
2	POLR2A	chr17:16944569-16944838	K562	blood:	n/a	n/a
3	MAFK	chr17:16944519-16945546	IMR90	lung:	n/a	chr17:16945082-16945097
4	JUND	chr17:16944545-16945019	A549	lung:	n/a	n/a
5	POLR2A	chr17:16944366-16945696	U87	brain:	n/a	n/a
6	SP1	chr17:16944243-16945770	A549	lung:	n/a	chr17:16945700-16945712 chr17:16945702-16945711 chr17:16945459-16945473 chr17:16945700-16945712 chr17:16945701-16945710 chr17:16944956-16944970 chr17:16945606-16945615 chr17:16945701-16945710 chr17:16945610-16945631 chr17:16945605-16945614 chr17:16945604-16945616 chr17:16945604-16945616
7	MXI1	chr17:16944242-16948097	SK-N-SH	brain:	n/a	n/a
8	MAX	chr17:16944484-16944935	SK-N-SH	brain:	n/a	n/a
9	SIN3AK20	chr17:16944503-16944817	HepG2	liver:	n/a	n/a
10	FOSL2	chr17:16944231-16945608	A549	lung:	n/a	chr17:16945166-16945176 chr17:16945166-16945176
11	POLR2A	chr17:16944360-16945696	U87	brain:	n/a	n/a
12	MAX	chr17:16944474-16944900	K562	blood:	n/a	n/a
13	MAX	chr17:16944412-16944874	ECC-1	luminal epithelium:	n/a	n/a
14	MXI1	chr17:16944131-16947555	IMR90	lung:	n/a	n/a
15	MAX	chr17:16944284-16944997	HCT-116	colon:	n/a	n/a
16	MXI1	chr17:16944456-16945709	H1-hESC	embryonic stem cell:	n/a	n/a
17	MXI1	chr17:16944369-16945837	HepG2	liver:	n/a	n/a
18	MXI1	chr17:16944558-16945715	Hela-S3	cervix:	n/a	n/a
19	SIN3AK20	chr17:16944520-16944774	HepG2	liver:	n/a	n/a
20	MAZ	chr17:16944585-16944786	K562	blood:	n/a	n/a
21	E2F6	chr17:16944548-16944748	K562	blood:	n/a	n/a
22	MYC	chr17:16944515-16944870	K562	blood:	n/a	n/a
23	JUND	chr17:16944581-16945727	K562	blood:	n/a	chr17:16945166-16945176 chr17:16945166-16945176
24	BHLHE40	chr17:16944614-16944869	K562	blood:	n/a	n/a
25	MAX	chr17:16944404-16945753	K562	blood:	n/a	n/a
26	ZNF384	chr17:16944373-16944731	K562	blood:	n/a	n/a
27	MAX	chr17:16944292-16945900	HCT-116	colon:	n/a	n/a
28	REST	chr17:16944231-16945821	H1-neurons	neurons:	n/a	n/a
29	MAX	chr17:16944311-16944938	HepG2	liver:	n/a	n/a
30	SIN3AK20	chr17:16944411-16945643	A549	lung:	n/a	n/a
31	SIN3AK20	chr17:16944568-16944753	SK-N-SH	brain:	n/a	n/a
32	MAX	chr17:16944327-16945838	A549	lung:	n/a	n/a
33	RCOR1	chr17:16944604-16944736	HepG2	liver:	n/a	n/a
34	MAX	chr17:16944541-16945748	Hela-S3	cervix:	n/a	n/a
35	EP300	chr17:16944348-16944788	HepG2	liver:	n/a	n/a
36	SIN3AK20	chr17:16944521-16944785	PFSK-1	brain:	n/a	n/a
37	RUNX3	chr17:16944283-16944733	GM12878	blood:	n/a	n/a
38	SIN3AK20	chr17:16944490-16944781	K562	blood:	n/a	n/a
39	KAP1	chr17:16944433-16945448	HEK293	kidney:	n/a	n/a
40	MAX	chr17:16944232-16945904	A549	lung:	n/a	n/a
41	SIN3AK20	chr17:16944466-16944822	H1-hESC	embryonic stem cell:	n/a	n/a
42	RAD21	chr17:16944576-16944645	HepG2	liver:	n/a	n/a
43	MYC	chr17:16944541-16945319	MCF10A-Er-Src	breast:	n/a	n/a
44	ZNF263	chr17:16944536-16945520	HEK293-T-REx	kidney:	n/a	chr17:16945232-16945253 chr17:16944846-16944855
45	RCOR1	chr17:16944564-16945702	K562	blood:	n/a	n/a
46	JUND	chr17:16944358-16944774	HepG2	liver:	n/a	n/a
47	SIN3AK20	chr17:16944475-16944900	SK-N-SH	brain:	n/a	n/a
48	PBX3	chr17:16944424-16945946	SK-N-SH	brain:	n/a	chr17:16945663-16945672 chr17:16945667-16945687
49	MAX	chr17:16944479-16944871	HepG2	liver:	n/a	n/a
50	MAX	chr17:16944524-16944849	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:16943176..16945630-chr17:17102978..17105800,2	K562	blood:
2	chr17:16944536..16947207-chr17:17109103..17111480,2	MCF-7	breast:
3	chr17:16930112..16931615-chr17:16942008..16944719,2	K562	blood:
4	chr17:16944416..16947050-chr17:16979219..16983384,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TNFRSF13B-3	chr17:16944523-16944627	XLOC_012406

Variant related genes	Relation type
MPRIP	TF binding region
ENSG00000225442	Chromatin interaction
ENSG00000179598	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10852843	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs10852845	0.85[ASN][1000 genomes]
rs11078364	0.93[ASN][1000 genomes]
rs11078365	0.97[ASN][1000 genomes]
rs11078366	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.97[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11078370	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11078375	1.00[CHB][hapmap]
rs11651460	1.00[CHB][hapmap];0.96[CHD][hapmap]
rs11651988	0.95[ASN][1000 genomes]
rs11652756	0.90[ASN][1000 genomes]
rs11652936	0.88[ASN][1000 genomes]
rs11654247	1.00[CHB][hapmap]
rs11654360	0.95[ASN][1000 genomes]
rs11654562	0.90[CHB][hapmap];0.93[ASN][1000 genomes]
rs11658084	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12450109	0.90[ASN][1000 genomes]
rs12450213	0.85[ASN][1000 genomes]
rs12450238	0.97[ASN][1000 genomes]
rs12450467	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12451054	0.88[ASN][1000 genomes]
rs12452303	0.90[ASN][1000 genomes]
rs12601325	1.00[CHB][hapmap]
rs12601422	0.87[MEX][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs12602124	0.95[ASN][1000 genomes]
rs12602129	0.95[ASN][1000 genomes]
rs16961288	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs16961412	1.00[CHB][hapmap];0.96[CHD][hapmap]
rs1877631	1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[LWK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs3744133	1.00[CHB][hapmap];0.96[CHD][hapmap]
rs3744140	1.00[CHB][hapmap];0.96[CHD][hapmap]
rs4073940	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4074611	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4264448	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4275916	0.88[ASN][1000 genomes]
rs4606773	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4621033	0.88[ASN][1000 genomes]
rs4985695	0.88[ASN][1000 genomes]
rs4985697	0.88[ASN][1000 genomes]
rs4985698	0.85[ASN][1000 genomes]
rs4985712	0.97[ASN][1000 genomes]
rs4985714	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4985715	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4985719	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4985723	0.86[ASN][1000 genomes]
rs4985727	0.88[ASN][1000 genomes]
rs4985739	1.00[CHB][hapmap];0.96[CHD][hapmap]
rs56009207	0.95[ASN][1000 genomes]
rs58472573	0.88[ASN][1000 genomes]
rs58814183	0.96[ASN][1000 genomes]
rs7207187	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7210339	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7217970	1.00[CHB][hapmap];0.96[CHD][hapmap]
rs7223583	0.95[ASN][1000 genomes]
rs7223686	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7223924	0.95[ASN][1000 genomes]
rs73979053	0.97[ASN][1000 genomes]
rs73979054	1.00[ASN][1000 genomes]
rs73979058	0.96[ASN][1000 genomes]
rs73979061	0.88[ASN][1000 genomes]
rs73979081	0.88[ASN][1000 genomes]
rs73979082	0.88[ASN][1000 genomes]
rs73979083	0.88[ASN][1000 genomes]
rs8067563	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs8075751	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.82[YRI][hapmap];0.97[ASN][1000 genomes]
rs9910011	0.97[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	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11658904	C3orf51	trans	cerebellum	SCAN
rs11658904	M-RIP	Cis_1M	lymphoblastoid	RTeQTL
rs11658904	LOC162632	cis	parietal	SCAN
rs11658904	MPRIP	cis	lymphoblastoid	seeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16935800-16945200	Weak transcription	Aorta	Aorta
2	chr17:16936000-16944800	Weak transcription	Brain Angular Gyrus	brain
3	chr17:16936000-16944800	Weak transcription	Esophagus	oesophagus
4	chr17:16936200-16944800	Weak transcription	HUVEC	blood vessel
5	chr17:16940400-16944800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr17:16940400-16944800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr17:16940400-16944800	Weak transcription	Right Atrium	heart
8	chr17:16940600-16944800	Weak transcription	Primary B cells from cord blood	blood
9	chr17:16940600-16944800	Weak transcription	Primary B cells from peripheral blood	blood
10	chr17:16940600-16945000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr17:16941800-16945000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr17:16942000-16945000	Enhancers	Fetal Intestine Large	intestine
13	chr17:16942600-16945000	Enhancers	Fetal Intestine Small	intestine
14	chr17:16943200-16945000	Enhancers	Fetal Muscle Trunk	muscle
15	chr17:16943200-16945000	Enhancers	Fetal Muscle Leg	muscle
16	chr17:16943400-16945000	Enhancers	Fetal Brain Male	brain
17	chr17:16943600-16945000	Weak transcription	Ovary	ovary
18	chr17:16944200-16944800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr17:16944200-16944800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr17:16944200-16944800	Enhancers	Stomach Smooth Muscle	stomach
21	chr17:16944200-16944800	Flanking Active TSS	HepG2	liver
22	chr17:16944200-16944800	Enhancers	NHLF	lung
23	chr17:16944200-16945000	Enhancers	HMEC	breast
24	chr17:16944200-16945000	Enhancers	NHDF-Ad	bronchial
25	chr17:16944200-16945200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr17:16944200-16945200	Enhancers	Placenta	Placenta
27	chr17:16944200-16945400	Flanking Active TSS	HSMM	muscle
28	chr17:16944400-16944800	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr17:16944400-16944800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr17:16944400-16944800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
31	chr17:16944400-16944800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr17:16944400-16944800	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr17:16944400-16944800	Active TSS	Brain Inferior Temporal Lobe	brain
34	chr17:16944400-16944800	Enhancers	Colon Smooth Muscle	Colon
35	chr17:16944400-16944800	Active TSS	Psoas Muscle	Psoas
36	chr17:16944400-16944800	Enhancers	NHEK	skin
37	chr17:16944400-16944800	Enhancers	Osteobl	bone
38	chr17:16944400-16945000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
39	chr17:16944400-16945000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr17:16944400-16945000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr17:16944400-16945000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr17:16944400-16945000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
43	chr17:16944400-16945000	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr17:16944400-16945000	Enhancers	Brain Substantia Nigra	brain
45	chr17:16944400-16945000	Enhancers	Right Ventricle	heart
46	chr17:16944400-16945000	Enhancers	Stomach Mucosa	stomach
47	chr17:16944400-16945200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr17:16944400-16945200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr17:16944400-16945200	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr17:16944400-16945200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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