Variant report

Variant	rs3923984
Chromosome Location	chr1:9653835-9653836
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	REST	chr1:9653456-9653886	SK-N-SH	brain:	n/a	chr1:9653716-9653736 chr1:9653720-9653733 chr1:9653722-9653731
2	REST	chr1:9653587-9653845	A549	lung:	n/a	chr1:9653716-9653736 chr1:9653720-9653733 chr1:9653722-9653731
3	REST	chr1:9653510-9653836	PFSK-1	brain:	n/a	chr1:9653716-9653736 chr1:9653720-9653733 chr1:9653722-9653731
4	REST	chr1:9653552-9653861	SK-N-SH	brain:	n/a	chr1:9653716-9653736 chr1:9653720-9653733 chr1:9653722-9653731
5	REST	chr1:9653405-9654022	PFSK-1	brain:	n/a	chr1:9653716-9653736 chr1:9653720-9653733 chr1:9653722-9653731
6	MAX	chr1:9653455-9654136	NB4	blood:	n/a	chr1:9653986-9653999 chr1:9653699-9653709 chr1:9653989-9653996 chr1:9653987-9653998 chr1:9653986-9654001 chr1:9653988-9653997 chr1:9653603-9653613 chr1:9653988-9653998
7	REST	chr1:9653515-9653972	HL-60	blood:	n/a	chr1:9653716-9653736 chr1:9653720-9653733 chr1:9653722-9653731
8	RCOR1	chr1:9653414-9653845	K562	blood:	n/a	n/a
9	KAP1	chr1:9653397-9653977	U2OS	brain:	n/a	n/a
10	REST	chr1:9653482-9653855	K562	blood:	n/a	chr1:9653716-9653736 chr1:9653720-9653733 chr1:9653722-9653731
11	REST	chr1:9653575-9653856	HepG2	liver:	n/a	chr1:9653716-9653736 chr1:9653720-9653733 chr1:9653722-9653731
12	RFX5	chr1:9653496-9653835	H1-hESC	embryonic stem cell:	n/a	chr1:9653646-9653661 chr1:9653648-9653663 chr1:9653649-9653663 chr1:9653651-9653660
13	REST	chr1:9653508-9653857	H1-hESC	embryonic stem cell:	n/a	chr1:9653716-9653736 chr1:9653720-9653733 chr1:9653722-9653731
14	RFX5	chr1:9653415-9653889	HepG2	liver:	n/a	chr1:9653646-9653661 chr1:9653648-9653663 chr1:9653649-9653663 chr1:9653651-9653660
15	GABPA	chr1:9653399-9653888	K562	blood:	n/a	chr1:9653699-9653708
16	REST	chr1:9653455-9654006	ECC-1	luminal epithelium:	n/a	chr1:9653716-9653736 chr1:9653720-9653733 chr1:9653722-9653731
17	ELF1	chr1:9653364-9653850	K562	blood:	n/a	chr1:9653610-9653623
18	HCFC1	chr1:9653530-9653840	K562	blood:	n/a	n/a
19	SIN3A	chr1:9653560-9653922	GM12878	blood:	n/a	chr1:9653722-9653732
20	SIN3AK20	chr1:9653444-9653900	K562	blood:	n/a	n/a
21	RFX5	chr1:9653472-9653853	GM12878	blood:	n/a	chr1:9653646-9653661 chr1:9653648-9653663 chr1:9653649-9653663 chr1:9653651-9653660
22	EP300	chr1:9653413-9653861	HepG2	liver:	n/a	n/a
23	REST	chr1:9653403-9654152	U87	brain:	n/a	chr1:9653716-9653736 chr1:9653720-9653733 chr1:9653722-9653731
24	RUNX3	chr1:9653564-9653902	GM12878	blood:	n/a	n/a
25	CBX3	chr1:9653370-9653868	K562	blood:	n/a	n/a
26	MAX	chr1:9653169-9654138	K562	blood:	n/a	chr1:9653986-9653999 chr1:9653699-9653709 chr1:9653989-9653996 chr1:9653987-9653998 chr1:9653986-9654001 chr1:9653988-9653997 chr1:9653603-9653613 chr1:9653988-9653998
27	YY1	chr1:9653389-9653914	K562	blood:	n/a	n/a
28	RFX5	chr1:9653337-9653948	IMR90	lung:	n/a	chr1:9653646-9653661 chr1:9653648-9653663 chr1:9653649-9653663 chr1:9653651-9653660
29	STAT2	chr1:9653494-9653871	K562	blood:	n/a	chr1:9653688-9653695
30	SIN3A	chr1:9653516-9654339	H1-hESC	embryonic stem cell:	n/a	chr1:9653722-9653732
31	MXI1	chr1:9653522-9653844	K562	blood:	n/a	chr1:9653645-9653660
32	RFX5	chr1:9653116-9654125	SK-N-SH	brain:	n/a	chr1:9653646-9653661 chr1:9653648-9653663 chr1:9653649-9653663 chr1:9653651-9653660
33	REST	chr1:9653442-9653960	K562	blood:	n/a	chr1:9653716-9653736 chr1:9653720-9653733 chr1:9653722-9653731
34	ZNF143	chr1:9653610-9653847	K562	blood:	n/a	n/a
35	POLR2A	chr1:9653739-9653837	K562	blood:	n/a	n/a
36	REST	chr1:9653401-9654154	U87	brain:	n/a	chr1:9653716-9653736 chr1:9653720-9653733 chr1:9653722-9653731
37	REST	chr1:9653493-9653926	MCF-7	breast:	n/a	chr1:9653716-9653736 chr1:9653720-9653733 chr1:9653722-9653731
38	POLR2A	chr1:9653342-9653845	H1-neurons	neurons:	n/a	n/a
39	REST	chr1:9653501-9653897	H1-hESC	embryonic stem cell:	n/a	chr1:9653716-9653736 chr1:9653720-9653733 chr1:9653722-9653731
40	REST	chr1:9653478-9654082	PFSK-1	brain:	n/a	chr1:9653716-9653736 chr1:9653720-9653733 chr1:9653722-9653731
41	MXI1	chr1:9653458-9653943	HepG2	liver:	n/a	chr1:9653645-9653660
42	POLR2A	chr1:9653444-9654282	K562	blood:	n/a	n/a
43	MXI1	chr1:9652920-9654531	SK-N-SH	brain:	n/a	chr1:9653645-9653660
44	RUNX3	chr1:9653486-9653880	GM12878	blood:	n/a	n/a
45	MYBL2	chr1:9653428-9653910	HepG2	liver:	n/a	n/a
46	REST	chr1:9653419-9654223	HL-60	blood:	n/a	chr1:9653716-9653736 chr1:9653720-9653733 chr1:9653722-9653731
47	NR2F2	chr1:9653158-9654133	K562	blood:	n/a	n/a
48	ELF1	chr1:9653176-9653962	GM12878	blood:	n/a	chr1:9653610-9653623
49	REST	chr1:9653592-9653846	GM12878	blood:	n/a	chr1:9653716-9653736 chr1:9653720-9653733 chr1:9653722-9653731
50	MXI1	chr1:9653549-9653884	GM12878	blood:	n/a	chr1:9653645-9653660

No.	Distal block	Cell Line	Cell type
1	chr1:9653517..9656272-chr1:9667967..9669548,2	MCF-7	breast:
2	chr1:9651551..9654296-chr1:9656942..9660108,3	MCF-7	breast:
3	chr1:9600120..9603287-chr1:9652178..9655376,3	K562	blood:
4	chr1:9652545..9654379-chr1:9656311..9658340,2	MCF-7	breast:

Variant related genes	Relation type
TMEM201	TF binding region
ENSG00000188807	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10864429	0.93[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12022881	0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs12023288	1.00[CEU][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[EUR][1000 genomes]
rs12037667	0.86[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.96[TSI][hapmap];0.86[ASN][1000 genomes]
rs12040542	0.86[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.86[ASN][1000 genomes]
rs12045459	0.83[EUR][1000 genomes]
rs12045493	0.84[EUR][1000 genomes]
rs12070568	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12084279	0.85[ASN][1000 genomes]
rs28719694	0.86[EUR][1000 genomes]
rs4073710	0.82[CEU][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4074744	1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4244632	0.80[JPT][hapmap]
rs4423053	0.94[CEU][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs4926482	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55655211	0.86[ASN][1000 genomes]
rs55687246	0.84[ASN][1000 genomes]
rs55780537	0.86[ASN][1000 genomes]
rs55986711	0.86[ASN][1000 genomes]
rs56026893	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56053581	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57272167	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58478478	0.85[ASN][1000 genomes]
rs60744607	0.85[ASN][1000 genomes]
rs6540961	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6540962	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6675436	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6698575	1.00[ASW][hapmap];0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72646709	0.86[ASN][1000 genomes]
rs72646712	0.86[ASN][1000 genomes]
rs72646713	0.86[ASN][1000 genomes]
rs72646715	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72646718	0.88[EUR][1000 genomes]
rs7364899	0.83[ASW][hapmap];0.81[MKK][hapmap]
rs7411273	1.00[ASW][hapmap];0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7525099	0.85[ASN][1000 genomes]
rs7544083	0.94[CEU][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9430152	0.94[CEU][hapmap];0.81[GIH][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9430153	0.94[CEU][hapmap];0.82[GIH][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs9430174	0.94[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9430180	0.94[EUR][1000 genomes]
rs9430181	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9430182	0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9430183	0.83[ASN][1000 genomes]
rs9430184	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9430273	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9430274	0.94[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9430332	0.94[CEU][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs9430369	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931984	chr1:8879337-9694749	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	570 gene(s)	inside rSNPs	diseases
2	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
3	nsv1013224	chr1:9441040-9699768	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv464283	chr1:9495571-9677853	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv545363	chr1:9495571-9677853	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv871521	chr1:9640291-9666364	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3923984	HNRNPCL1	cis	cerebellum	SCAN
rs3923984	NPPA	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9649800-9654400	Enhancers	Spleen	Spleen
2	chr1:9649800-9657200	Enhancers	Fetal Heart	heart
3	chr1:9649800-9657400	Enhancers	Placenta	Placenta
4	chr1:9649800-9657400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr1:9650000-9654000	Enhancers	HSMMtube	muscle
6	chr1:9650000-9654200	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr1:9650000-9654200	Enhancers	Primary B cells from cord blood	blood
8	chr1:9650000-9654200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:9650000-9654200	Enhancers	Left Ventricle	heart
10	chr1:9650000-9654400	Enhancers	Right Atrium	heart
11	chr1:9650000-9655400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:9650000-9656000	Enhancers	Psoas Muscle	Psoas
13	chr1:9650000-9661200	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr1:9650200-9654400	Enhancers	Adipose Nuclei	Adipose
15	chr1:9650200-9654600	Enhancers	H1 Cell Line	embryonic stem cell
16	chr1:9650200-9654600	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr1:9650200-9654600	Enhancers	Esophagus	oesophagus
18	chr1:9650200-9655400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:9650200-9656800	Weak transcription	Aorta	Aorta
20	chr1:9650200-9657000	Enhancers	Right Ventricle	heart
21	chr1:9650400-9654000	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr1:9650400-9654200	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr1:9650400-9655600	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr1:9650400-9655600	Enhancers	Fetal Muscle Trunk	muscle
25	chr1:9650400-9656200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:9650400-9676000	Weak transcription	A549	lung
27	chr1:9650600-9654200	Enhancers	Brain Substantia Nigra	brain
28	chr1:9650600-9654600	Enhancers	Fetal Brain Male	brain
29	chr1:9650800-9656200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr1:9651000-9654400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
31	chr1:9651200-9654200	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr1:9651400-9654600	Enhancers	Brain Germinal Matrix	brain
33	chr1:9651400-9654600	Enhancers	Fetal Thymus	thymus
34	chr1:9651400-9672000	Weak transcription	Hela-S3	cervix
35	chr1:9651600-9654200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr1:9651600-9655800	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr1:9651800-9654400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:9651800-9656200	Enhancers	Fetal Muscle Leg	muscle
39	chr1:9652000-9654200	Enhancers	Brain Angular Gyrus	brain
40	chr1:9652000-9654400	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr1:9652000-9654800	Enhancers	Fetal Brain Female	brain
42	chr1:9652200-9654000	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr1:9652200-9654200	Enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr1:9652200-9654200	Enhancers	K562	blood
45	chr1:9652200-9654400	Enhancers	Primary T cells fromperipheralblood	blood
46	chr1:9652200-9654400	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr1:9652200-9654400	Enhancers	Colonic Mucosa	Colon
48	chr1:9652200-9654400	Enhancers	Fetal Intestine Small	intestine
49	chr1:9652200-9654400	Enhancers	Fetal Lung	lung
50	chr1:9652200-9654600	Enhancers	iPS-15b Cell Line	embryonic stem cell

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