Variant report

Variant	rs12107408
Chromosome Location	chr3:99903390-99903391
allele	C/G
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	chr3:99903386-99903436	HNPCEpiC	eye:	n/a
2	chr3:99903386-99903436	HUVEC	blood vessel:	n/a
3	chr3:99903386-99903436	NHDF-neo	bronchial:	n/a
4	chr3:99903386-99903436	Hela-S3	cervix:	n/a
5	chr3:99903386-99903436	HAEpiC	amniotic membrane:	n/a
6	chr3:99903386-99903436	HRE	kidney:	n/a
7	chr3:99903386-99903436	SK-N-SH_RA	brain:	n/a
8	chr3:99903386-99903436	HCPEpiC	choroid plexus:	n/a
9	chr3:99903386-99903436	ProgFib	skin:	n/a
10	chr3:99903386-99903436	SK-N-MC	brain:	n/a
11	chr3:99903386-99903436	U87	brain:	n/a
12	chr3:99903386-99903436	BJ	skin:	n/a
13	chr3:99903386-99903436	NB4	blood:	n/a
14	chr3:99903386-99903436	SKMC	muscle:	n/a
15	chr3:99903386-99903436	HRCEpiC	kidney:	n/a
16	chr3:99903386-99903436	GM12891	blood:	n/a
17	chr3:99903386-99903436	SAEC	small airway:	n/a
18	chr3:99903386-99903436	HL-60	blood:	n/a
19	chr3:99903386-99903436	AG04450	lung:	fetal
20	chr3:99903386-99903436	HEEpiC	esophagus:	n/a
21	chr3:99903386-99903436	Caco-2	colon:	n/a
22	chr3:99903386-99903436	HCM	heart:	n/a
23	chr3:99903386-99903436	PANC-1	pancreas:	n/a
24	chr3:99903386-99903436	H1-hESC	embryonic stem cell:	embryo
25	chr3:99903386-99903436	HMEC	breast:	n/a
26	chr3:99903386-99903436	AG09319	gingival:	n/a
27	chr3:99903386-99903436	MCF10A-Er-Src	breast:	n/a
28	chr3:99903386-99903436	HIPEpiC	eye:	n/a
29	chr3:99903386-99903436	BE2_C	brain:	n/a
30	chr3:99903386-99903436	GM12892	blood:	n/a
31	chr3:99903386-99903436	ovcar-3	ovarian:	n/a
32	chr3:99903386-99903436	AoSMC	blood vessel:	n/a
33	chr3:99903386-99903436	IMR90	lung:	fetal
34	chr3:99903386-99903436	AG10803	skin:	n/a
35	chr3:99903386-99903436	A549	lung:	n/a
36	chr3:99903386-99903436	HEK293	kidney:	embryo
37	chr3:99903386-99903436	Hepatocyte	liver:	n/a
38	chr3:99903386-99903436	T-47D	breast:	n/a
39	chr3:99903386-99903436	MCF-7	breast:	n/a
40	chr3:99903386-99903436	GM19239	blood:	n/a
41	chr3:99903386-99903436	NT2-D1	testis:	n/a
42	chr3:99903386-99903436	ECC-1	luminal epithelium:	n/a
43	chr3:99903386-99903436	NH-A	brain:	n/a
44	chr3:99903386-99903436	RPTEC	kidney:	n/a
45	chr3:99903386-99903436	NHBE	bronchial:	n/a
46	chr3:99903386-99903436	CMK	blood:	n/a
47	chr3:99903386-99903436	Jurkat	blood:	n/a
48	chr3:99903386-99903436	GM06990	blood:	n/a
49	chr3:99903386-99903436	HepG2	liver:	n/a
50	chr3:99903386-99903436	GM12878	blood:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:99901097..99903790-chr3:99904221..99907015,2	K562	blood:

No data

Variant related genes	Relation type
TMEM30C	CpG island
ENSG00000235156	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2583657	1.00[EUR][1000 genomes]
rs7431827	0.88[YRI][hapmap]
rs7641782	0.94[YRI][hapmap];0.82[AFR][1000 genomes]
rs7652706	1.00[YRI][hapmap]
rs9872339	0.83[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1008483	chr3:99660754-99903769	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1010897	chr3:99660754-99904783	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv591148	chr3:99774720-99905803	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99877600-99904600	Weak transcription	Right Ventricle	heart
2	chr3:99892600-99904200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr3:99895000-99904600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:99898600-99903800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr3:99898600-99904200	Weak transcription	Ovary	ovary
6	chr3:99899000-99903800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr3:99899000-99904200	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr3:99899000-99904200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr3:99899000-99904200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr3:99899000-99907800	Weak transcription	Psoas Muscle	Psoas
11	chr3:99899000-99911000	Weak transcription	Aorta	Aorta
12	chr3:99899200-99903800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr3:99899200-99904200	Weak transcription	Left Ventricle	heart
14	chr3:99899400-99903600	Weak transcription	Fetal Lung	lung
15	chr3:99899400-99903800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr3:99899400-99904000	Weak transcription	Duodenum Mucosa	Duodenum
17	chr3:99899600-99903800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr3:99899600-99903800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr3:99899600-99904200	Weak transcription	Fetal Muscle Leg	muscle
20	chr3:99899600-99904400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr3:99899800-99903800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:99900400-99904000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:99902400-99903400	Enhancers	HUES48 Cell Line	embryonic stem cell
24	chr3:99902400-99903600	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr3:99902400-99904000	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr3:99902400-99905800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:99902600-99903800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr3:99902600-99904800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:99902800-99904000	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr3:99902800-99904200	Weak transcription	Spleen	Spleen
31	chr3:99902800-99905000	Enhancers	Fetal Stomach	stomach
32	chr3:99903000-99905600	Enhancers	NHDF-Ad	bronchial
33	chr3:99903200-99904800	Enhancers	Adipose Nuclei	Adipose

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