Variant report

Variant	rs12058316
Chromosome Location	chr1:58326491-58326492
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:19)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr1:58325857-58326506	H1-neurons	neurons:	n/a	n/a
2	TCF12	chr1:58326070-58326547	SK-N-SH	brain:	n/a	n/a
3	REST	chr1:58325846-58326623	H1-neurons	neurons:	n/a	n/a
4	GATA3	chr1:58326041-58326574	SK-N-SH	brain:	n/a	n/a

No data

No data

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C8A-4	chr1:58326260-58326544	ENSG00000226759
2	lnc-C8A-4	chr1:58326309-58326598	ENSG00000226759
3	lnc-C8A-4	chr1:58326215-58326705	ENSG00000226759
4	lnc-C8A-4	chr1:58326253-58326591	ENSG00000226759
5	lnc-C8A-4	chr1:58326204-58326705	ENSG00000226759.3
6	lnc-C8A-4	chr1:58326204-58326598	ENSG00000226759.3
7	lnc-C8A-4	chr1:58326229-58326591	ENSG00000226759.3
8	lnc-C8A-4	chr1:58326234-58326581	ENSG00000226759.3
9	lnc-C8A-4	chr1:58326253-58326607	ENSG00000226759.3
10	lnc-C8A-4	chr1:58326261-58326544	NONHSAT003486
11	lnc-C8A-4	chr1:58326266-58326544	NONHSAT003487
12	lnc-C8A-4	chr1:58326336-58326705	ENSG00000226759.3
13	lnc-C8A-4	chr1:58326215-58326581	NR_104364
14	lnc-C8A-4	chr1:58326215-58326591	NR_104363
15	lnc-C8A-4	chr1:58326215-58326544	NR_104365
16	lnc-C8A-4	chr1:58326239-58326591	ENSG00000226759.3
17	lnc-C8A-4	chr1:58326311-58326598	ENSG00000226759.3
18	lnc-C8A-4	chr1:58326281-58326705	ENSG00000226759.3
19	lnc-C8A-4	chr1:58326253-58326544	ENSG00000226759.3

No data

No data

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11207113	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs11207116	0.86[AFR][1000 genomes]
rs11207120	0.86[AFR][1000 genomes]
rs11207123	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11207125	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12063361	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12072058	0.90[AFR][1000 genomes]
rs12077887	1.00[AMR][1000 genomes]
rs12078749	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs12081343	0.87[YRI][hapmap]
rs12081493	1.00[YRI][hapmap]
rs12084446	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12086375	0.92[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12086654	1.00[MKK][hapmap];0.85[YRI][hapmap]
rs12092417	0.82[YRI][hapmap]
rs12092824	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6679423	1.00[AFR][1000 genomes]
rs6695286	1.00[LWK][hapmap];1.00[MKK][hapmap];0.87[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015057	chr1:57976993-58793962	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv530017	chr1:58002290-58669736	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv431379	chr1:58224212-58802608	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv829937	chr1:58258288-58406506	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58320800-58330400	Weak transcription	Fetal Brain Male	brain
2	chr1:58322400-58327000	Enhancers	HMEC	breast
3	chr1:58322600-58327000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:58324600-58326600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:58325600-58326800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:58325600-58327200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:58325800-58326600	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr1:58325800-58326800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:58326000-58326800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr1:58326000-58327000	Enhancers	Placenta	Placenta
11	chr1:58326200-58326800	Enhancers	Fetal Intestine Large	intestine
12	chr1:58326200-58327000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:58326200-58327200	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr1:58326400-58327200	Enhancers	NHEK	skin
15	chr1:58326400-58327400	Enhancers	Fetal Intestine Small	intestine

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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