Variant report

Variant	rs11654342
Chromosome Location	chr17:46126689-46126690
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	chr17:46124277-46126855	GM12892	blood:	n/a	n/a
2	MYC	chr17:46124582-46126769	A549	lung:	n/a	chr17:46125917-46125927 chr17:46125705-46125715 chr17:46125209-46125219 chr17:46125627-46125637
3	MAX	chr17:46124297-46126790	A549	lung:	n/a	chr17:46125917-46125927 chr17:46125705-46125715 chr17:46125209-46125219 chr17:46125627-46125637
4	POU2F2	chr17:46126076-46126831	GM12891	blood:	n/a	chr17:46126671-46126682 chr17:46126673-46126682 chr17:46126654-46126664 chr17:46126673-46126683 chr17:46126671-46126682 chr17:46126673-46126683 chr17:46126674-46126681 chr17:46126647-46126669 chr17:46126668-46126686 chr17:46126672-46126682 chr17:46126673-46126681 chr17:46126670-46126685
5	POLR2A	chr17:46124467-46126786	K562	blood:	n/a	n/a
6	FOXA1	chr17:46125265-46126699	HepG2	liver:	n/a	chr17:46126388-46126403
7	BCLAF1	chr17:46126078-46126814	GM12878	blood:	n/a	n/a
8	FOXA2	chr17:46125002-46126764	A549	lung:	n/a	n/a
9	TAF1	chr17:46125983-46126725	GM12878	blood:	n/a	n/a
10	NFIC	chr17:46125977-46126800	GM12878	blood:	n/a	n/a
11	RELA	chr17:46124707-46126736	GM15510	blood:	n/a	n/a
12	POLR2A	chr17:46124715-46126831	GM12892	blood:	n/a	n/a
13	PML	chr17:46126037-46126712	GM12878	blood:	n/a	n/a
14	MAFK	chr17:46125070-46126730	Hela-S3	cervix:	n/a	chr17:46125227-46125242 chr17:46125139-46125154
15	POLR2A	chr17:46124024-46126770	PFSK-1	brain:	n/a	n/a
16	YY1	chr17:46124759-46126694	GM12891	blood:	n/a	chr17:46125747-46125761 chr17:46125178-46125186 chr17:46125179-46125189 chr17:46125674-46125685 chr17:46125180-46125188 chr17:46125167-46125189 chr17:46125756-46125765 chr17:46125172-46125191 chr17:46125913-46125927 chr17:46125626-46125640 chr17:46125744-46125758 chr17:46125974-46125988 chr17:46125975-46125989 chr17:46125707-46125716 chr17:46125171-46125191
17	FOXM1	chr17:46126029-46126779	GM12878	blood:	n/a	n/a
18	POU2F2	chr17:46126022-46126777	GM12878	blood:	n/a	chr17:46126671-46126682 chr17:46126673-46126682 chr17:46126654-46126664 chr17:46126673-46126683 chr17:46126671-46126682 chr17:46126673-46126683 chr17:46126674-46126681 chr17:46126647-46126669 chr17:46126668-46126686 chr17:46126672-46126682 chr17:46126673-46126681 chr17:46126670-46126685
19	TAF1	chr17:46124548-46126753	GM12878	blood:	n/a	n/a
20	POU2F2	chr17:46126344-46126773	GM12891	blood:	n/a	chr17:46126671-46126682 chr17:46126673-46126682 chr17:46126654-46126664 chr17:46126673-46126683 chr17:46126671-46126682 chr17:46126673-46126683 chr17:46126674-46126681 chr17:46126647-46126669 chr17:46126668-46126686 chr17:46126672-46126682 chr17:46126673-46126681 chr17:46126670-46126685
21	SIN3AK20	chr17:46123914-46126967	MCF-7	breast:	n/a	n/a
22	MAX	chr17:46124406-46126833	HCT-116	colon:	n/a	chr17:46125917-46125927 chr17:46125705-46125715 chr17:46125209-46125219 chr17:46125627-46125637
23	POLR2A	chr17:46124215-46126844	U87	brain:	n/a	n/a
24	POLR2A	chr17:46124342-46126773	Raji	blood:	n/a	n/a
25	POLR2A	chr17:46124261-46126838	U87	brain:	n/a	n/a
26	POLR2A	chr17:46124613-46126790	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr17:46124572-46126821	GM19099	blood:	n/a	n/a
28	MXI1	chr17:46121714-46126967	SK-N-SH	brain:	n/a	n/a
29	POLR2A	chr17:46125638-46126757	GM12891	blood:	n/a	n/a
30	MAZ	chr17:46124849-46126768	GM12878	blood:	n/a	chr17:46125917-46125927 chr17:46125705-46125715 chr17:46125627-46125637
31	POLR2A	chr17:46124794-46126795	GM15510	blood:	n/a	n/a
32	REST	chr17:46124284-46126689	A549	lung:	n/a	chr17:46125042-46125062 chr17:46125048-46125062
33	YY1	chr17:46124544-46126734	SK-N-SH	brain:	n/a	chr17:46125747-46125761 chr17:46125178-46125186 chr17:46125179-46125189 chr17:46125674-46125685 chr17:46125180-46125188 chr17:46125167-46125189 chr17:46125756-46125765 chr17:46125172-46125191 chr17:46125913-46125927 chr17:46125626-46125640 chr17:46125744-46125758 chr17:46125974-46125988 chr17:46125975-46125989 chr17:46125707-46125716 chr17:46125171-46125191
34	ELF1	chr17:46124833-46126764	MCF-7	breast:	n/a	chr17:46125628-46125640 chr17:46125756-46125765 chr17:46125751-46125763 chr17:46125225-46125237
35	TCF12	chr17:46124520-46126712	A549	lung:	n/a	n/a
36	GABPA	chr17:46124721-46126725	SK-N-SH	brain:	n/a	chr17:46125707-46125716
37	POLR2A	chr17:46124776-46126810	GM18526	blood:	n/a	n/a
38	POU2F2	chr17:46126463-46126745	GM12878	blood:	n/a	chr17:46126671-46126682 chr17:46126673-46126682 chr17:46126654-46126664 chr17:46126673-46126683 chr17:46126671-46126682 chr17:46126673-46126683 chr17:46126674-46126681 chr17:46126647-46126669 chr17:46126668-46126686 chr17:46126672-46126682 chr17:46126673-46126681 chr17:46126670-46126685
39	POLR2A	chr17:46124849-46126726	HUVEC	blood vessel:	n/a	n/a
40	ZNF384	chr17:46126452-46126837	GM12878	blood:	n/a	n/a
41	TBL1XR1	chr17:46124600-46126750	GM12878	blood:	n/a	n/a
42	ZKSCAN1	chr17:46124992-46126732	Hela-S3	cervix:	n/a	n/a
43	MAX	chr17:46124739-46126737	ECC-1	luminal epithelium:	n/a	chr17:46125917-46125927 chr17:46125705-46125715 chr17:46125209-46125219 chr17:46125627-46125637
44	HEY1	chr17:46125135-46126834	HepG2	liver:	n/a	chr17:46125975-46125990 chr17:46125973-46125988 chr17:46125917-46125932 chr17:46125939-46125954
45	POLR2A	chr17:46124809-46126810	U87	brain:	n/a	n/a
46	POLR2A	chr17:46124507-46126790	GM12878	blood:	n/a	n/a
47	POLR2A	chr17:46122734-46126909	MCF10A-Er-Src	breast:	n/a	n/a
48	CHD1	chr17:46124061-46127653	IMR90	lung:	n/a	chr17:46125708-46125718
49	YY1	chr17:46125991-46126816	GM12878	blood:	n/a	n/a
50	MYC	chr17:46124541-46126704	NB4	blood:	n/a	chr17:46125917-46125927 chr17:46125705-46125715 chr17:46125209-46125219 chr17:46125627-46125637

No.	Distal block	Cell Line	Cell type
1	chr17:46124778..46127532-chr17:46702734..46705232,2	K562	blood:
2	chr17:46048551..46050173-chr17:46123931..46126830,2	MCF-7	breast:
3	chr17:46125014..46129511-chr17:46182877..46189561,8	K562	blood:
4	chr17:46123351..46126971-chr17:46177351..46182209,7	K562	blood:
5	chr17:46125721..46126711-chr6:53659755..53660427,2	Hela-S3	cervix:
6	chr17:45769138..45771658-chr17:46124750..46126805,2	MCF-7	breast:
7	chr1:25756460..25757141-chr17:46126080..46126905,2	Hela-S3	cervix:
8	chr17:46124892..46127654-chr17:46182877..46187326,5	K562	blood:
9	chr17:46124025..46127922-chr17:46176725..46180326,7	MCF-7	breast:
10	chr17:46123925..46127532-chr17:46701622..46704234,4	K562	blood:
11	chr17:46043414..46046355-chr17:46124548..46126704,2	MCF-7	breast:
12	chr17:46125402..46127552-chr17:46984446..46987320,2	K562	blood:
13	chr17:46125418..46126971-chr17:46177352..46179960,2	K562	blood:
14	chr17:46126076..46126786-chr7:112090237..112090948,2	Hela-S3	cervix:
15	chr10:116286194..116286857-chr17:46126211..46126989,2	Hela-S3	cervix:
16	chr17:46124943..46127247-chr17:46188061..46189641,2	K562	blood:
17	chr17:46047400..46050259-chr17:46124707..46126731,3	MCF-7	breast:
18	chr17:46123538..46128867-chr17:46183649..46187295,7	MCF-7	breast:
19	chr17:46021116..46023804-chr17:46125669..46127456,2	K562	blood:
20	chr17:46122869..46127022-chr17:46176971..46180616,11	MCF-7	breast:
21	chr17:46124694..46126922-chr17:46984422..46985932,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000263412	TF binding region
ENSG00000108468	Chromatin interaction
ENSG00000159202	Chromatin interaction
ENSG00000188672	Chromatin interaction
ENSG00000099204	Chromatin interaction
ENSG00000263798	Chromatin interaction
ENSG00000108465	Chromatin interaction
ENSG00000006652	Chromatin interaction
ENSG00000137269	Chromatin interaction
ENSG00000248278	Chromatin interaction
ENSG00000170689	Chromatin interaction
ENSG00000198933	Chromatin interaction
ENSG00000002919	Chromatin interaction
ENSG00000108439	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11079813	0.84[AMR][1000 genomes]
rs11650615	0.88[AFR][1000 genomes]
rs11654292	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11658242	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12103808	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1544597	0.80[AMR][1000 genomes]
rs56258199	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60843764	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6504067	0.84[AMR][1000 genomes]
rs7207553	0.84[AMR][1000 genomes]
rs7210671	0.84[AMR][1000 genomes]
rs7219844	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7220398	0.82[AMR][1000 genomes]
rs7221720	0.82[AMR][1000 genomes]
rs7221897	0.84[AMR][1000 genomes]
rs7222646	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7224155	0.84[AMR][1000 genomes]
rs7225288	0.82[AMR][1000 genomes]
rs73322881	0.84[AMR][1000 genomes]
rs73322886	0.84[AMR][1000 genomes]
rs8065797	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8067470	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8071697	0.84[AMR][1000 genomes]
rs8073220	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9890850	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9893110	0.84[AMR][1000 genomes]
rs9900074	0.82[AFR][1000 genomes]
rs9905800	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9909922	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469808	chr17:46049868-46228673	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv482897	chr17:46049868-46228673	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11654342	RP5-890E16.2	cis	Nerve Tibial	GTEx
rs11654342	PNPO	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46123600-46127200	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr17:46123800-46127000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr17:46123800-46127600	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr17:46124000-46127200	Active TSS	H1 Cell Line	embryonic stem cell
5	chr17:46124000-46127200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr17:46124000-46127200	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr17:46124200-46126800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr17:46124200-46127200	Active TSS	GM12878-XiMat	blood
9	chr17:46124200-46127400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr17:46124200-46128000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr17:46124200-46128400	Active TSS	HSMMtube	muscle
12	chr17:46124400-46126800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr17:46124400-46127200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr17:46124400-46127200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr17:46124400-46127400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr17:46124400-46127400	Active TSS	H9 Cell Line	embryonic stem cell
17	chr17:46124400-46127600	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr17:46124400-46127600	Active TSS	Right Ventricle	heart
19	chr17:46124400-46127800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr17:46124400-46128200	Active TSS	Left Ventricle	heart
21	chr17:46124400-46132200	Active TSS	Psoas Muscle	Psoas
22	chr17:46124600-46126800	Active TSS	Esophagus	oesophagus
23	chr17:46124600-46127000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr17:46124600-46127000	Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr17:46124600-46127000	Active TSS	Brain Cingulate Gyrus	brain
26	chr17:46124600-46127200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
27	chr17:46124600-46127200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr17:46124600-46127200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr17:46124600-46127200	Active TSS	Aorta	Aorta
30	chr17:46124600-46127200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
31	chr17:46124600-46127200	Active TSS	K562	blood
32	chr17:46124600-46127400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr17:46124600-46127400	Active TSS	Ovary	ovary
34	chr17:46124600-46127600	Active TSS	iPS-18 Cell Line	embryonic stem cell
35	chr17:46124600-46127600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr17:46124600-46127800	Active TSS	iPS-15b Cell Line	embryonic stem cell
37	chr17:46124600-46128000	Active TSS	Fetal Kidney	kidney
38	chr17:46124600-46129600	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr17:46124800-46126800	Active TSS	Duodenum Mucosa	Duodenum
40	chr17:46124800-46126800	Active TSS	Stomach Mucosa	stomach
41	chr17:46124800-46127000	Active TSS	Brain Hippocampus Middle	brain
42	chr17:46124800-46127000	Active TSS	Brain Substantia Nigra	brain
43	chr17:46124800-46127000	Active TSS	Colonic Mucosa	Colon
44	chr17:46124800-46127000	Active TSS	Fetal Intestine Large	intestine
45	chr17:46124800-46127000	Active TSS	Lung	lung
46	chr17:46124800-46127000	Active TSS	Rectal Smooth Muscle	rectum
47	chr17:46124800-46127000	Active TSS	Small Intestine	intestine
48	chr17:46124800-46127000	Active TSS	Stomach Smooth Muscle	stomach
49	chr17:46124800-46127000	Active TSS	Spleen	Spleen
50	chr17:46124800-46127000	Active TSS	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links