Variant report

Variant	rs7247201
Chromosome Location	chr19:40724776-40724777
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:61)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr19:40721702-40725011	PANC-1	pancreas:	n/a	chr19:40721931-40721944
2	POLR2A	chr19:40724474-40724892	PFSK-1	brain:	n/a	n/a
3	REST	chr19:40721693-40724914	PANC-1	pancreas:	n/a	chr19:40721931-40721944
4	REST	chr19:40723809-40724891	A549	lung:	n/a	n/a
5	REST	chr19:40723799-40724890	PANC-1	pancreas:	n/a	n/a
6	SIN3AK20	chr19:40721650-40725020	PANC-1	pancreas:	n/a	n/a
7	REST	chr19:40721682-40727491	PANC-1	pancreas:	n/a	chr19:40721931-40721944 chr19:40726153-40726161
8	REST	chr19:40721744-40727478	PANC-1	pancreas:	n/a	chr19:40721931-40721944 chr19:40726153-40726161
9	CTCF	chr19:40722434-40725120	A549	lung:	n/a	chr19:40723352-40723365 chr19:40723444-40723457 chr19:40723442-40723458

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:40724733-40724783	Hepatocyte	liver:	n/a
2	chr19:40724733-40724783	HCM	heart:	n/a
3	chr19:40724733-40724783	BJ	skin:	n/a
4	chr19:40724733-40724783	GM12891	blood:	n/a
5	chr19:40724733-40724783	MCF10A-Er-Src	breast:	n/a
6	chr19:40724733-40724783	HEK293	kidney:	embryo
7	chr19:40724733-40724783	HCT-116	colon:	n/a
8	chr19:40724733-40724783	GM19239	blood:	n/a
9	chr19:40724733-40724783	U87	brain:	n/a
10	chr19:40724733-40724783	Jurkat	blood:	n/a
11	chr19:40724733-40724783	HIPEpiC	eye:	n/a
12	chr19:40724733-40724783	AG04450	lung:	fetal
13	chr19:40724733-40724783	SAEC	small airway:	n/a
14	chr19:40724733-40724783	SK-N-SH	brain:	n/a
15	chr19:40724733-40724783	MCF-7	breast:	n/a
16	chr19:40724733-40724783	GM12892	blood:	n/a
17	chr19:40724733-40724783	HCF	heart:	n/a
18	chr19:40724733-40724783	Caco-2	colon:	n/a
19	chr19:40724733-40724783	ProgFib	skin:	n/a
20	chr19:40724733-40724783	AG10803	skin:	n/a
21	chr19:40724733-40724783	GM12878	blood:	n/a
22	chr19:40724733-40724783	SK-N-SH_RA	brain:	n/a
23	chr19:40724733-40724783	PFSK-1	brain:	n/a
24	chr19:40724733-40724783	CMK	blood:	n/a
25	chr19:40724733-40724783	NHDF-neo	bronchial:	n/a
26	chr19:40724733-40724783	T-47D	breast:	n/a
27	chr19:40724733-40724783	Hela-S3	cervix:	n/a
28	chr19:40724733-40724783	HL-60	blood:	n/a
29	chr19:40724733-40724783	NH-A	brain:	n/a
30	chr19:40724733-40724783	NB4	blood:	n/a
31	chr19:40724733-40724783	IMR90	lung:	fetal
32	chr19:40724733-40724783	HCPEpiC	choroid plexus:	n/a
33	chr19:40724733-40724783	HRPEpiC	eye:	n/a
34	chr19:40724733-40724783	AG09309	skin:	n/a
35	chr19:40724733-40724783	H1-hESC	embryonic stem cell:	embryo
36	chr19:40724733-40724783	RPTEC	kidney:	n/a
37	chr19:40724733-40724783	ECC-1	luminal epithelium:	n/a
38	chr19:40724733-40724783	AoSMC	blood vessel:	n/a
39	chr19:40724733-40724783	NT2-D1	testis:	n/a
40	chr19:40724733-40724783	NHBE	bronchial:	n/a
41	chr19:40724733-40724783	K562	blood:	n/a
42	chr19:40724733-40724783	SKMC	muscle:	n/a
43	chr19:40724733-40724783	HRCEpiC	kidney:	n/a
44	chr19:40724733-40724783	HAEpiC	amniotic membrane:	n/a
45	chr19:40724733-40724783	PrEC	prostate:	n/a
46	chr19:40724733-40724783	BE2_C	brain:	n/a
47	chr19:40724733-40724783	HNPCEpiC	eye:	n/a
48	chr19:40724733-40724783	GM06990	blood:	n/a
49	chr19:40724733-40724783	SK-N-MC	brain:	n/a
50	chr19:40724733-40724783	LNCaP	prostate:	n/a

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:40724342..40727794-chr19:40739430..40743149,3	K562	blood:
2	chr19:40722262..40725312-chr19:40726429..40730380,4	MCF-7	breast:
3	chr19:40723230..40725206-chr19:40730553..40733160,2	MCF-7	breast:
4	chr19:40719578..40724896-chr19:40726262..40733162,10	MCF-7	breast:
5	chr19:40697008..40699890-chr19:40723055..40726049,3	MCF-7	breast:
6	chr19:40723301..40724804-chr20:35806454..35807992,2	K562	blood:

No data

Variant related genes	Relation type
TTC9B	TF binding region
TTC9B	CpG island
ENSG00000105219	Chromatin interaction
ENSG00000101353	Chromatin interaction
ENSG00000105221	Chromatin interaction
ENSG00000118705	Chromatin interaction
ENSG00000130758	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10402740	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1129156	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12971806	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12975651	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs189281	0.93[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2304184	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2304189	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2356229	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs339522	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs339523	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs339525	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs339526	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3746005	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4239504	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4490099	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4530264	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4802070	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803320	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56694147	0.83[ASN][1000 genomes]
rs7252471	0.82[EUR][1000 genomes]
rs7258548	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7260249	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8106744	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9749056	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv2758499	chr19:40612420-40839520	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv2758761	chr19:40612420-40839520	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv911698	chr19:40689580-40725304	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	diseases
5	nsv911699	chr19:40691632-40816530	Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	nsv911700	chr19:40695598-40725304	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv911701	chr19:40695598-40728417	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv911702	chr19:40697061-40731371	Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv911703	chr19:40711333-40730279	Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv911704	chr19:40716652-40730279	Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases
11	nsv911705	chr19:40716652-40731371	ZNF genes & repeats Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases
12	esv1833489	chr19:40722123-40923908	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer 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	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40711200-40731800	Weak transcription	Right Atrium	heart
2	chr19:40713200-40725200	Weak transcription	Hela-S3	cervix
3	chr19:40718600-40725200	Weak transcription	Dnd41	blood
4	chr19:40723400-40724800	Active TSS	Brain Cingulate Gyrus	brain
5	chr19:40723600-40724800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr19:40723600-40724800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
7	chr19:40723600-40725200	Weak transcription	K562	blood
8	chr19:40723800-40729000	Weak transcription	Gastric	stomach
9	chr19:40724000-40724800	Active TSS	Brain Anterior Caudate	brain
10	chr19:40724200-40729000	Weak transcription	Pancreas	Pancrea
11	chr19:40724400-40724800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
12	chr19:40724400-40724800	Flanking Active TSS	Fetal Brain Male	brain
13	chr19:40724400-40725000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr19:40724400-40725400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr19:40724400-40725400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr19:40724600-40724800	Flanking Active TSS	Fetal Brain Female	brain
17	chr19:40724600-40725600	Weak transcription	Brain Angular Gyrus	brain
18	chr19:40724600-40726000	Enhancers	Cortex derived primary cultured neurospheres	brain

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