Variant report

Variant	rs1535340
Chromosome Location	chr14:36983798-36983799
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SUZ12	chr14:36981170-36992861	NT2-D1	testis:	n/a	n/a
2	SUZ12	chr14:36981289-36984664	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTBP2	chr14:36981433-36984746	H1-hESC	embryonic stem cell:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr14:36983791-36983841	MCF10A-Er-Src	breast:	n/a
2	chr14:36983791-36983841	MCF-7	breast:	n/a
3	chr14:36983791-36983841	Hepatocyte	liver:	n/a
4	chr14:36983791-36983841	ECC-1	luminal epithelium:	n/a
5	chr14:36983791-36983841	SK-N-SH_RA	brain:	n/a
6	chr14:36983791-36983841	Hela-S3	cervix:	n/a
7	chr14:36983791-36983841	NB4	blood:	n/a
8	chr14:36983791-36983841	HNPCEpiC	eye:	n/a
9	chr14:36983791-36983841	GM12891	blood:	n/a
10	chr14:36983791-36983841	AG04450	lung:	fetal
11	chr14:36983791-36983841	H1-hESC	embryonic stem cell:	embryo
12	chr14:36983791-36983841	HEK293	kidney:	embryo
13	chr14:36983791-36983841	AG10803	skin:	n/a
14	chr14:36983791-36983841	HL-60	blood:	n/a
15	chr14:36983791-36983841	HMEC	breast:	n/a
16	chr14:36983791-36983841	HCT-116	colon:	n/a
17	chr14:36983791-36983841	BE2_C	brain:	n/a
18	chr14:36983791-36983841	BJ	skin:	n/a
19	chr14:36983791-36983841	GM19239	blood:	n/a
20	chr14:36983791-36983841	SK-N-SH	brain:	n/a
21	chr14:36983791-36983841	HEEpiC	esophagus:	n/a
22	chr14:36983791-36983841	GM12878	blood:	n/a
23	chr14:36983791-36983841	AG04449	skin:	fetal
24	chr14:36983791-36983841	HRPEpiC	eye:	n/a
25	chr14:36983791-36983841	HepG2	liver:	n/a
26	chr14:36983791-36983841	ovcar-3	ovarian:	n/a
27	chr14:36983791-36983841	Jurkat	blood:	n/a
28	chr14:36983791-36983841	T-47D	breast:	n/a
29	chr14:36983791-36983841	SAEC	small airway:	n/a
30	chr14:36983791-36983841	HCM	heart:	n/a
31	chr14:36983791-36983841	SKMC	muscle:	n/a
32	chr14:36983791-36983841	AG09309	skin:	n/a
33	chr14:36983791-36983841	HPAEpiC	pulmonary alveolar:	n/a
34	chr14:36983791-36983841	CMK	blood:	n/a
35	chr14:36983791-36983841	SK-N-MC	brain:	n/a
36	chr14:36983791-36983841	HRCEpiC	kidney:	n/a
37	chr14:36983791-36983841	HCPEpiC	choroid plexus:	n/a
38	chr14:36983791-36983841	PrEC	prostate:	n/a
39	chr14:36983791-36983841	IMR90	lung:	fetal
40	chr14:36983791-36983841	RPTEC	kidney:	n/a
41	chr14:36983791-36983841	NHDF-neo	bronchial:	n/a
42	chr14:36983791-36983841	PANC-1	pancreas:	n/a
43	chr14:36983791-36983841	NT2-D1	testis:	n/a
44	chr14:36983791-36983841	GM12892	blood:	n/a
45	chr14:36983791-36983841	Caco-2	colon:	n/a
46	chr14:36983791-36983841	AG09319	gingival:	n/a
47	chr14:36983791-36983841	LNCaP	prostate:	n/a
48	chr14:36983791-36983841	HAEpiC	amniotic membrane:	n/a
49	chr14:36983791-36983841	HRE	kidney:	n/a
50	chr14:36983791-36983841	A549	lung:	n/a

No data

Variant related genes	Relation type
NKX2-1-AS1	TF binding region
SFTA3	TF binding region
NKX2-1-AS1	CpG island
SFTA3	CpG island

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1005343	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1005354	1.00[ASN][1000 genomes]
rs1005355	1.00[ASN][1000 genomes]
rs10143437	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10431615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10483474	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1535341	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1535342	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17104778	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17104780	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs17104802	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs177322	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs177325	1.00[ASN][1000 genomes]
rs1956966	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2057328	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs73253957	1.00[ASN][1000 genomes]
rs735599	1.00[ASN][1000 genomes]
rs735708	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8004831	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs8016238	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs927285	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap]
rs986876	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1040256	chr14:36501452-37172046	Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv542040	chr14:36501452-37172046	Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
3	nsv1047290	chr14:36564568-37445157	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
4	nsv1037952	chr14:36670484-37294692	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
5	nsv542042	chr14:36670484-37294692	Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
6	nsv1053685	chr14:36915643-37245920	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv917279	chr14:36953511-37146655	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:36981200-36985200	Active TSS	Lung	lung
2	chr14:36981400-36991200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
3	chr14:36982000-36984800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
4	chr14:36982000-36985000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
5	chr14:36982200-36984400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
6	chr14:36982400-36983800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr14:36982800-36984000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr14:36982800-36985400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr14:36983000-36984200	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
10	chr14:36983200-36984200	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr14:36983200-36984200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
12	chr14:36983200-36986200	Bivalent/Poised TSS	Fetal Lung	lung
13	chr14:36983400-36984000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
14	chr14:36983400-36984200	Bivalent Enhancer	Fetal Brain Male	brain
15	chr14:36983400-36984600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr14:36983600-36983800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
17	chr14:36983600-36983800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
18	chr14:36983600-36983800	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
19	chr14:36983600-36984000	Bivalent/Poised TSS	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links