Variant report

Variant	rs1017923
Chromosome Location	chr5:1967265-1967266
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr5:1967249-1967299	AG04449	skin:	fetal
2	chr5:1967249-1967299	GM19239	blood:	n/a
3	chr5:1967249-1967299	NHDF-neo	bronchial:	n/a
4	chr5:1967249-1967299	SK-N-SH_RA	brain:	n/a
5	chr5:1967249-1967299	Jurkat	blood:	n/a
6	chr5:1967249-1967299	BE2_C	brain:	n/a
7	chr5:1967249-1967299	SAEC	small airway:	n/a
8	chr5:1967249-1967299	BJ	skin:	n/a
9	chr5:1967249-1967299	HL-60	blood:	n/a
10	chr5:1967249-1967299	IMR90	lung:	fetal
11	chr5:1967249-1967299	AoSMC	blood vessel:	n/a
12	chr5:1967249-1967299	HUVEC	blood vessel:	n/a
13	chr5:1967249-1967299	HCF	heart:	n/a
14	chr5:1967249-1967299	HCM	heart:	n/a
15	chr5:1967249-1967299	SK-N-MC	brain:	n/a
16	chr5:1967249-1967299	PANC-1	pancreas:	n/a
17	chr5:1967249-1967299	SKMC	muscle:	n/a
18	chr5:1967249-1967299	HIPEpiC	eye:	n/a
19	chr5:1967249-1967299	CMK	blood:	n/a
20	chr5:1967249-1967299	NB4	blood:	n/a
21	chr5:1967249-1967299	HRCEpiC	kidney:	n/a
22	chr5:1967249-1967299	Caco-2	colon:	n/a
23	chr5:1967249-1967299	LNCaP	prostate:	n/a
24	chr5:1967249-1967299	AG09309	skin:	n/a
25	chr5:1967249-1967299	HepG2	liver:	n/a
26	chr5:1967249-1967299	RPTEC	kidney:	n/a
27	chr5:1967249-1967299	NHBE	bronchial:	n/a
28	chr5:1967249-1967299	A549	lung:	n/a
29	chr5:1967249-1967299	HCT-116	colon:	n/a
30	chr5:1967249-1967299	K562	blood:	n/a
31	chr5:1967249-1967299	GM12878	blood:	n/a
32	chr5:1967249-1967299	SK-N-SH	brain:	n/a
33	chr5:1967249-1967299	Hela-S3	cervix:	n/a
34	chr5:1967249-1967299	ProgFib	skin:	n/a
35	chr5:1967249-1967299	MCF10A-Er-Src	breast:	n/a
36	chr5:1967249-1967299	HRPEpiC	eye:	n/a
37	chr5:1967249-1967299	ovcar-3	ovarian:	n/a
38	chr5:1967249-1967299	NT2-D1	testis:	n/a
39	chr5:1967249-1967299	GM12891	blood:	n/a
40	chr5:1967249-1967299	ECC-1	luminal epithelium:	n/a
41	chr5:1967249-1967299	HPAEpiC	pulmonary alveolar:	n/a
42	chr5:1967249-1967299	AG09319	gingival:	n/a
43	chr5:1967249-1967299	HRE	kidney:	n/a
44	chr5:1967249-1967299	HMEC	breast:	n/a
45	chr5:1967249-1967299	GM12892	blood:	n/a
46	chr5:1967249-1967299	GM06990	blood:	n/a
47	chr5:1967249-1967299	AG10803	skin:	n/a
48	chr5:1967249-1967299	HEK293	kidney:	embryo
49	chr5:1967249-1967299	T-47D	breast:	n/a
50	chr5:1967249-1967299	H1-hESC	embryonic stem cell:	embryo

No data

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-IRX4-3	chr5:1967191-1967268	XLOC_004708

No data

Variant related genes	Relation type
ENSG00000249731	CpG island

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1601642	0.80[ASN][1000 genomes]
rs17611544	1.00[ASW][hapmap];0.85[CHB][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.80[TSI][hapmap];0.80[ASN][1000 genomes]
rs4975775	0.87[TSI][hapmap]
rs56246449	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58712170	0.87[EUR][1000 genomes]
rs73031910	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73031919	0.92[ASN][1000 genomes]
rs73031927	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73031929	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73031933	0.82[ASN][1000 genomes]
rs73031934	0.80[ASN][1000 genomes]
rs73031938	0.80[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	nsv817407	chr5:1495354-2191460	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
2	nsv869236	chr5:1719263-2259100	Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
3	nsv915846	chr5:1891098-2167677	Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1026930	chr5:1898993-2126061	Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv508344	chr5:1905222-1976860	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv881562	chr5:1907974-1976187	Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv427705	chr5:1950467-2115059	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1961200-1967800	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr5:1964000-1972800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:1964800-1967800	Enhancers	Fetal Muscle Trunk	muscle
4	chr5:1965200-1968400	Enhancers	Fetal Muscle Leg	muscle
5	chr5:1966000-1968200	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr5:1966200-1967400	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr5:1966200-1968200	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr5:1966400-1967600	Weak transcription	Dnd41	blood
9	chr5:1966600-1967400	Enhancers	iPS-15b Cell Line	embryonic stem cell
10	chr5:1966800-1967400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:1967000-1967800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr5:1967000-1973400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr5:1967000-1973800	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr5:1967200-1967600	Weak transcription	Fetal Stomach	stomach
15	chr5:1967200-1967800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr5:1967200-1968400	Enhancers	HMEC	breast

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