Variant report

Variant	rs16920473
Chromosome Location	chr9:104299293-104299294
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	YY1	chr9:104299250-104299583	GM12878	blood:	n/a	n/a
2	YY1	chr9:104299254-104299551	GM12891	blood:	n/a	n/a
3	REST	chr9:104298893-104299900	A549	lung:	n/a	chr9:104299413-104299422
4	YY1	chr9:104299272-104299585	H1-hESC	embryonic stem cell:	n/a	n/a
5	REST	chr9:104299139-104299605	A549	lung:	n/a	chr9:104299413-104299422
6	REST	chr9:104299125-104299591	PFSK-1	brain:	n/a	chr9:104299413-104299422
7	RCOR1	chr9:104299088-104299750	IMR90	lung:	n/a	n/a
8	MXI1	chr9:104299146-104299748	IMR90	lung:	n/a	n/a
9	REST	chr9:104299087-104299706	PFSK-1	brain:	n/a	chr9:104299413-104299422
10	BHLHE40	chr9:104299234-104299490	K562	blood:	n/a	n/a
11	REST	chr9:104299113-104299823	PANC-1	pancreas:	n/a	chr9:104299413-104299422
12	SIN3AK20	chr9:104299263-104299532	K562	blood:	n/a	n/a
13	REST	chr9:104299135-104299617	HepG2	liver:	n/a	chr9:104299413-104299422
14	REST	chr9:104299190-104299627	K562	blood:	n/a	chr9:104299413-104299422
15	REST	chr9:104299224-104299562	U87	brain:	n/a	chr9:104299413-104299422
16	REST	chr9:104299226-104299546	SK-N-SH	brain:	n/a	chr9:104299413-104299422
17	REST	chr9:104299050-104299673	GM12878	blood:	n/a	chr9:104299413-104299422
18	SIN3AK20	chr9:104299235-104299527	H1-hESC	embryonic stem cell:	n/a	n/a
19	REST	chr9:104299232-104299507	GM12878	blood:	n/a	chr9:104299413-104299422
20	REST	chr9:104298892-104299956	ECC-1	luminal epithelium:	n/a	chr9:104299413-104299422
21	REST	chr9:104299259-104299484	GM12878	blood:	n/a	chr9:104299413-104299422
22	REST	chr9:104299206-104299571	PFSK-1	brain:	n/a	chr9:104299413-104299422
23	MXI1	chr9:104299273-104299487	H1-hESC	embryonic stem cell:	n/a	n/a
24	YY1	chr9:104299220-104299551	GM12892	blood:	n/a	n/a
25	RCOR1	chr9:104299265-104299535	GM12878	blood:	n/a	n/a
26	ZNF143	chr9:104299235-104299601	GM12878	blood:	n/a	n/a
27	SIN3A	chr9:104299210-104299596	H1-hESC	embryonic stem cell:	n/a	n/a
28	REST	chr9:104299193-104299562	U87	brain:	n/a	chr9:104299413-104299422
29	REST	chr9:104299092-104299630	U87	brain:	n/a	chr9:104299413-104299422
30	REST	chr9:104299159-104299778	H1-hESC	embryonic stem cell:	n/a	chr9:104299413-104299422
31	REST	chr9:104299201-104299630	Hela-S3	cervix:	n/a	chr9:104299413-104299422
32	YY1	chr9:104299187-104299564	H1-hESC	embryonic stem cell:	n/a	n/a
33	REST	chr9:104299285-104299496	PANC-1	pancreas:	n/a	chr9:104299413-104299422
34	REST	chr9:104299160-104299614	SK-N-SH	brain:	n/a	chr9:104299413-104299422
35	REST	chr9:104298900-104299843	K562	blood:	n/a	chr9:104299413-104299422
36	REST	chr9:104299198-104299539	PANC-1	pancreas:	n/a	chr9:104299413-104299422
37	REST	chr9:104299219-104299555	PFSK-1	brain:	n/a	chr9:104299413-104299422
38	YY1	chr9:104299257-104299559	ECC-1	luminal epithelium:	n/a	n/a
39	REST	chr9:104299226-104299539	HepG2	liver:	n/a	chr9:104299413-104299422
40	YY1	chr9:104299211-104299554	ECC-1	luminal epithelium:	n/a	n/a
41	YY1	chr9:104299255-104299492	A549	lung:	n/a	n/a
42	REST	chr9:104299244-104299535	HepG2	liver:	n/a	chr9:104299413-104299422
43	REST	chr9:104299090-104299630	U87	brain:	n/a	chr9:104299413-104299422
44	REST	chr9:104298859-104299967	ECC-1	luminal epithelium:	n/a	chr9:104299413-104299422
45	REST	chr9:104299227-104299588	GM12878	blood:	n/a	chr9:104299413-104299422
46	ZNF143	chr9:104299290-104299475	Hela-S3	cervix:	n/a	n/a
47	E2F4	chr9:104299281-104299478	MCF10A-Er-Src	breast:	n/a	n/a
48	REST	chr9:104299069-104299704	HepG2	liver:	n/a	chr9:104299413-104299422
49	MXI1	chr9:104299212-104299499	GM12878	blood:	n/a	n/a
50	TEAD4	chr9:104299141-104299732	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:104295154..104296821-chr9:104298164..104300262,2	MCF-7	breast:
2	chr9:104288484..104290134-chr9:104298816..104300608,2	K562	blood:

Variant related genes	Relation type
TMEM246	TF binding region
ENSG00000165152	Chromatin interaction
ENSG00000155827	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10115763	0.89[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs10125893	0.81[AMR][1000 genomes]
rs10989553	0.81[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.93[MEX][hapmap];0.88[ASN][1000 genomes]
rs12342026	0.85[ASN][1000 genomes]
rs12342991	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12343288	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12347518	0.89[ASN][1000 genomes]
rs13284984	0.90[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13290720	0.92[ASW][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13295809	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs1885977	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1929496	0.92[ASW][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28533545	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34153995	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34727333	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36004060	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3739722	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs3739723	0.87[JPT][hapmap]
rs3739724	0.82[JPT][hapmap]
rs3824473	0.89[CHB][hapmap];0.94[CHD][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs3903804	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4119332	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs45488691	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59770438	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7030238	0.89[CHB][hapmap];0.94[CHD][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs7034754	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9299345	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046975	chr9:104167583-104659873	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv893626	chr9:104172936-104324545	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv949579	chr9:104229820-104512923	Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv1052492	chr9:104263419-104387782	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv893627	chr9:104268342-104334333	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16920473	SEC61B	cis	cerebellum	SCAN
rs16920473	FOXE1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:104296600-104301800	Weak transcription	Spleen	Spleen
2	chr9:104296800-104299400	Enhancers	Primary T killer memory cells from peripheral blood	blood
3	chr9:104296800-104300400	Enhancers	Fetal Heart	heart
4	chr9:104296800-104300600	Weak transcription	Esophagus	oesophagus
5	chr9:104296800-104302600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr9:104296800-104302600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr9:104296800-104302600	Weak transcription	Lung	lung
8	chr9:104296800-104302800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr9:104296800-104302800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:104296800-104305800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr9:104296800-104334200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr9:104296800-104337400	Weak transcription	Stomach Mucosa	stomach
13	chr9:104297000-104299400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr9:104297000-104302000	Weak transcription	Fetal Stomach	stomach
15	chr9:104297000-104302600	Weak transcription	Colonic Mucosa	Colon
16	chr9:104297000-104302600	Weak transcription	NH-A	brain
17	chr9:104297000-104302800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr9:104297000-104302800	Weak transcription	HSMMtube	muscle
19	chr9:104297000-104309200	Weak transcription	HUVEC	blood vessel
20	chr9:104297000-104317600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr9:104297200-104299600	Enhancers	HMEC	breast
22	chr9:104297200-104302400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr9:104297200-104302600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr9:104297200-104302800	Weak transcription	Fetal Intestine Small	intestine
25	chr9:104297200-104309200	Weak transcription	K562	blood
26	chr9:104297400-104299400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
27	chr9:104297400-104301400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
28	chr9:104297600-104299400	Genic enhancers	HSMM	muscle
29	chr9:104297600-104299600	Genic enhancers	Brain Angular Gyrus	brain
30	chr9:104297600-104299600	Genic enhancers	Rectal Smooth Muscle	rectum
31	chr9:104297600-104300400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr9:104297600-104300400	Strong transcription	Sigmoid Colon	Sigmoid Colon
33	chr9:104297600-104300800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
34	chr9:104297600-104300800	Strong transcription	Osteobl	bone
35	chr9:104297600-104301000	Genic enhancers	Brain Cingulate Gyrus	brain
36	chr9:104297600-104301000	Strong transcription	Fetal Muscle Trunk	muscle
37	chr9:104297600-104302800	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr9:104297600-104304600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr9:104297600-104306000	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr9:104297600-104321200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
41	chr9:104297600-104330400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr9:104297600-104330400	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr9:104297800-104299400	Enhancers	Muscle Satellite Cultured Cells	--
44	chr9:104297800-104299400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr9:104297800-104299400	Genic enhancers	Brain Substantia Nigra	brain
46	chr9:104297800-104299600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr9:104297800-104299600	Genic enhancers	Primary T cells fromperipheralblood	blood
48	chr9:104297800-104299600	Genic enhancers	Brain Hippocampus Middle	brain
49	chr9:104297800-104300400	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr9:104297800-104300800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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