Variant report

Variant	rs4516035
Chromosome Location	chr12:48299826-48299827
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:11)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:48298208-48300165	A549	lung:	n/a	chr12:48299217-48299233

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:48299800-48299850	HNPCEpiC	eye:	n/a
2	chr12:48299800-48299850	HRPEpiC	eye:	n/a
3	chr12:48299800-48299850	SK-N-SH_RA	brain:	n/a
4	chr12:48299800-48299850	HIPEpiC	eye:	n/a
5	chr12:48299800-48299850	GM06990	blood:	n/a
6	chr12:48299800-48299850	U87	brain:	n/a
7	chr12:48299800-48299850	AG04450	lung:	fetal
8	chr12:48299800-48299850	NT2-D1	testis:	n/a
9	chr12:48299800-48299850	AoSMC	blood vessel:	n/a
10	chr12:48299800-48299850	GM19239	blood:	n/a
11	chr12:48299800-48299850	Hela-S3	cervix:	n/a
12	chr12:48299800-48299850	HL-60	blood:	n/a
13	chr12:48299800-48299850	RPTEC	kidney:	n/a
14	chr12:48299800-48299850	HCM	heart:	n/a
15	chr12:48299800-48299850	PrEC	prostate:	n/a
16	chr12:48299800-48299850	HCT-116	colon:	n/a
17	chr12:48299800-48299850	AG04449	skin:	fetal
18	chr12:48299800-48299850	PFSK-1	brain:	n/a
19	chr12:48299800-48299850	NHBE	bronchial:	n/a
20	chr12:48299800-48299850	SKMC	muscle:	n/a
21	chr12:48299800-48299850	BJ	skin:	n/a
22	chr12:48299800-48299850	PANC-1	pancreas:	n/a
23	chr12:48299800-48299850	MCF10A-Er-Src	breast:	n/a
24	chr12:48299800-48299850	HCPEpiC	choroid plexus:	n/a
25	chr12:48299800-48299850	GM12892	blood:	n/a
26	chr12:48299800-48299850	A549	lung:	n/a
27	chr12:48299800-48299850	HEK293	kidney:	embryo
28	chr12:48299800-48299850	HRE	kidney:	n/a
29	chr12:48299800-48299850	ECC-1	luminal epithelium:	n/a
30	chr12:48299800-48299850	HRCEpiC	kidney:	n/a
31	chr12:48299800-48299850	HepG2	liver:	n/a
32	chr12:48299800-48299850	SAEC	small airway:	n/a
33	chr12:48299800-48299850	GM12891	blood:	n/a
34	chr12:48299800-48299850	NH-A	brain:	n/a
35	chr12:48299800-48299850	AG10803	skin:	n/a
36	chr12:48299800-48299850	AG09319	gingival:	n/a
37	chr12:48299800-48299850	CMK	blood:	n/a
38	chr12:48299800-48299850	IMR90	lung:	fetal
39	chr12:48299800-48299850	H1-hESC	embryonic stem cell:	embryo
40	chr12:48299800-48299850	HUVEC	blood vessel:	n/a
41	chr12:48299800-48299850	Hepatocyte	liver:	n/a
42	chr12:48299800-48299850	SK-N-SH	brain:	n/a
43	chr12:48299800-48299850	NHDF-neo	bronchial:	n/a
44	chr12:48299800-48299850	SK-N-MC	brain:	n/a
45	chr12:48299800-48299850	HMEC	breast:	n/a
46	chr12:48299800-48299850	ProgFib	skin:	n/a
47	chr12:48299800-48299850	HAEpiC	amniotic membrane:	n/a
48	chr12:48299800-48299850	HPAEpiC	pulmonary alveolar:	n/a
49	chr12:48299800-48299850	MCF-7	breast:	n/a
50	chr12:48299800-48299850	NB4	blood:	n/a

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:48221119..48223794-chr12:48297710..48299941,2	MCF-7	breast:
2	chr12:48275805..48279171-chr12:48299207..48301457,3	K562	blood:
3	chr12:48146667..48149507-chr12:48298293..48300492,2	MCF-7	breast:
4	chr12:48297320..48300707-chr12:48356346..48358827,3	MCF-7	breast:
5	chr12:48296295..48301288-chr12:48356017..48360451,6	MCF-7	breast:
6	chr12:48299753..48302171-chr12:48303242..48305976,2	K562	blood:
7	chr12:48297838..48300182-chr12:48335522..48337383,2	MCF-7	breast:
8	chr12:48211668..48213938-chr12:48298192..48300037,2	MCF-7	breast:
9	chr12:48290096..48306593-chr12:48332606..48350271,44	MCF-7	breast:
10	chr12:48296929..48299891-chr12:48498540..48500341,2	MCF-7	breast:
11	chr12:48298891..48301417-chr12:48363482..48365531,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM106C-3	chr12:48298888-48301381	NONHSAT027959

No data

Variant related genes	Relation type
VDR	TF binding region
VDR	CpG island
ENSG00000134291	Chromatin interaction
ENSG00000061273	Chromatin interaction
ENSG00000211584	Chromatin interaction
ENSG00000257488	Chromatin interaction
ENSG00000111424	Chromatin interaction
ENSG00000205537	Chromatin interaction
ENSG00000079387	Chromatin interaction
ENSG00000152556	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10875696	1.00[CHB][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168297	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11614332	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4760658	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[ASN][1000 genomes]
rs4760671	0.82[ASW][hapmap];0.96[GIH][hapmap];0.94[MEX][hapmap];1.00[YRI][hapmap]
rs7139166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7296550	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7310552	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311856	0.82[ASW][hapmap];0.96[GIH][hapmap];0.88[MEX][hapmap];1.00[YRI][hapmap]
rs7970314	1.00[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428589	chr12:48282920-48341192	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4516035	C12orf68	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48297600-48300000	Active TSS	HSMMtube	muscle
2	chr12:48298000-48300000	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr12:48298600-48300000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
4	chr12:48298600-48300200	Active TSS	Duodenum Mucosa	Duodenum
5	chr12:48299000-48300000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
6	chr12:48299200-48300000	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr12:48299400-48300000	Bivalent Enhancer	Fetal Muscle Leg	muscle
8	chr12:48299400-48300200	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr12:48299600-48300000	Active TSS	Fetal Intestine Small	intestine
10	chr12:48299600-48300000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr12:48299600-48300000	Enhancers	Pancreas	Pancrea
12	chr12:48299600-48300200	Active TSS	Colonic Mucosa	Colon
13	chr12:48299600-48301000	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr12:48299600-48301200	Weak transcription	HepG2	liver
15	chr12:48299600-48301600	Weak transcription	Placenta	Placenta
16	chr12:48299600-48301800	Weak transcription	Liver	Liver
17	chr12:48299600-48303800	Weak transcription	Adipose Nuclei	Adipose
18	chr12:48299600-48303800	Weak transcription	Small Intestine	intestine
19	chr12:48299600-48304200	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr12:48299800-48300000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
21	chr12:48299800-48300000	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr12:48299800-48300000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:48299800-48300000	Enhancers	HMEC	breast
24	chr12:48299800-48303400	Weak transcription	NHEK	skin
25	chr12:48299800-48304000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links