Variant report

Variant	rs7411365
Chromosome Location	chr1:152780139-152780140
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:1)
LncRNA
region (count:0)
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	chr1:152780139-152780189	U87	brain:	n/a
2	chr1:152780139-152780189	CMK	blood:	n/a
3	chr1:152780139-152780189	Hela-S3	cervix:	n/a
4	chr1:152780139-152780189	SAEC	small airway:	n/a
5	chr1:152780139-152780189	SK-N-SH_RA	brain:	n/a
6	chr1:152780139-152780189	HCPEpiC	choroid plexus:	n/a
7	chr1:152780139-152780189	SKMC	muscle:	n/a
8	chr1:152780139-152780189	HAEpiC	amniotic membrane:	n/a
9	chr1:152780139-152780189	HPAEpiC	pulmonary alveolar:	n/a
10	chr1:152780139-152780189	IMR90	lung:	fetal
11	chr1:152780139-152780189	HepG2	liver:	n/a
12	chr1:152780139-152780189	Jurkat	blood:	n/a
13	chr1:152780139-152780189	GM19239	blood:	n/a
14	chr1:152780139-152780189	PANC-1	pancreas:	n/a
15	chr1:152780139-152780189	HMEC	breast:	n/a
16	chr1:152780139-152780189	HRE	kidney:	n/a
17	chr1:152780139-152780189	BJ	skin:	n/a
18	chr1:152780139-152780189	BE2_C	brain:	n/a
19	chr1:152780139-152780189	SK-N-SH	brain:	n/a
20	chr1:152780139-152780189	RPTEC	kidney:	n/a
21	chr1:152780139-152780189	HUVEC	blood vessel:	n/a
22	chr1:152780139-152780189	LNCaP	prostate:	n/a
23	chr1:152780139-152780189	AG09319	gingival:	n/a
24	chr1:152780139-152780189	HNPCEpiC	eye:	n/a
25	chr1:152780139-152780189	HCT-116	colon:	n/a
26	chr1:152780139-152780189	HL-60	blood:	n/a
27	chr1:152780139-152780189	Hepatocyte	liver:	n/a
28	chr1:152780139-152780189	K562	blood:	n/a
29	chr1:152780139-152780189	PFSK-1	brain:	n/a
30	chr1:152780139-152780189	NB4	blood:	n/a
31	chr1:152780139-152780189	PrEC	prostate:	n/a
32	chr1:152780139-152780189	HEEpiC	esophagus:	n/a
33	chr1:152780139-152780189	NH-A	brain:	n/a
34	chr1:152780139-152780189	AG09309	skin:	n/a
35	chr1:152780139-152780189	GM12891	blood:	n/a
36	chr1:152780139-152780189	HRCEpiC	kidney:	n/a
37	chr1:152780139-152780189	ECC-1	luminal epithelium:	n/a
38	chr1:152780139-152780189	HRPEpiC	eye:	n/a
39	chr1:152780139-152780189	MCF10A-Er-Src	breast:	n/a
40	chr1:152780139-152780189	SK-N-MC	brain:	n/a
41	chr1:152780139-152780189	NHBE	bronchial:	n/a
42	chr1:152780139-152780189	Caco-2	colon:	n/a
43	chr1:152780139-152780189	AoSMC	blood vessel:	n/a
44	chr1:152780139-152780189	HCF	heart:	n/a
45	chr1:152780139-152780189	AG04450	lung:	fetal
46	chr1:152780139-152780189	ovcar-3	ovarian:	n/a
47	chr1:152780139-152780189	HCM	heart:	n/a
48	chr1:152780139-152780189	HIPEpiC	eye:	n/a
49	chr1:152780139-152780189	A549	lung:	n/a
50	chr1:152780139-152780189	GM06990	blood:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:152775705..152778056-chr1:152780040..152782015,2	MCF-7	breast:

No data

Variant related genes	Relation type
LCE1C	CpG island
LCE1B	CpG island
ENSG00000197084	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1048534	0.89[ASW][hapmap];0.80[CEU][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes]
rs11205108	0.92[EUR][1000 genomes]
rs11205109	0.92[EUR][1000 genomes]
rs12036241	0.85[EUR][1000 genomes]
rs12046205	0.92[EUR][1000 genomes]
rs12046231	0.92[EUR][1000 genomes]
rs12046930	0.92[EUR][1000 genomes]
rs12094590	0.92[EUR][1000 genomes]
rs12568028	0.80[CEU][hapmap];0.81[TSI][hapmap];0.91[EUR][1000 genomes]
rs1332505	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs1412545	0.80[CEU][hapmap]
rs16834421	0.81[TSI][hapmap]
rs16834461	0.80[CEU][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs16834495	0.85[EUR][1000 genomes]
rs2297487	0.80[CEU][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs4845475	0.80[EUR][1000 genomes]
rs4845487	0.92[EUR][1000 genomes]
rs6698773	0.80[EUR][1000 genomes]
rs6701221	0.80[CEU][hapmap]
rs7549803	0.80[CEU][hapmap]
rs872180	0.85[EUR][1000 genomes]
rs913998	0.83[EUR][1000 genomes]
rs913999	0.83[EUR][1000 genomes]
rs944683	0.80[CEU][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs950337	0.89[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757755	chr1:152472839-152898153	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	esv2758970	chr1:152472839-152898153	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	nsv427786	chr1:152572990-152898153	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv1013433	chr1:152619305-153262215	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
5	nsv535170	chr1:152619305-153262215	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
6	nsv1001834	chr1:152648853-153279143	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
7	nsv428521	chr1:152663153-152831578	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
8	nsv947325	chr1:152670204-152793272	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv547899	chr1:152672005-153245082	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
10	esv2763813	chr1:152687058-152780522	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv508615	chr1:152724155-152787503	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
12	nsv1004884	chr1:152724514-152780522	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
13	nsv999918	chr1:152749733-152861866	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	esv1799675	chr1:152759643-152785456	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
15	nsv1007453	chr1:152761911-152780277	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
16	nsv997985	chr1:152761911-152780522	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
17	nsv1010346	chr1:152761911-152787707	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
18	nsv1012943	chr1:152762750-152787707	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
19	nsv1009885	chr1:152762750-152851273	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7411365	SPRR1A	cis	parietal	SCAN
rs7411365	LCE1F	cis	cerebellum	SCAN
rs7411365	LYSMD1	cis	parietal	SCAN
rs7411365	TPM3	cis	cerebellum	SCAN
rs7411365	JTB	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:152779400-152783600	Weak transcription	Esophagus	oesophagus
2	chr1:152779600-152783000	Weak transcription	NHEK	skin
3	chr1:152779600-152783200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:152779600-152783200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:152779600-152783400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:152779600-152783400	Weak transcription	HMEC	breast
7	chr1:152779600-152783600	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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