Variant report

Variant	rs12817104
Chromosome Location	chr12:48382573-48382574
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr12:48381933-48382621	ECC-1	luminal epithelium:	n/a	chr12:48382585-48382595
2	MAX	chr12:48382226-48382595	H1-hESC	embryonic stem cell:	n/a	chr12:48382370-48382379 chr12:48382366-48382375
3	REST	chr12:48382051-48382782	H1-neurons	neurons:	n/a	n/a
4	ZBTB7A	chr12:48381787-48382613	ECC-1	luminal epithelium:	n/a	n/a
5	SIN3A	chr12:48382230-48382596	H1-hESC	embryonic stem cell:	n/a	n/a
6	EP300	chr12:48381933-48382579	ECC-1	luminal epithelium:	n/a	chr12:48382138-48382152 chr12:48382144-48382158

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:48382534-48382584	Hela-S3	cervix:	n/a
2	chr12:48382534-48382584	PFSK-1	brain:	n/a
3	chr12:48382534-48382584	BE2_C	brain:	n/a
4	chr12:48382534-48382584	HCF	heart:	n/a
5	chr12:48382534-48382584	ovcar-3	ovarian:	n/a
6	chr12:48382534-48382584	Hepatocyte	liver:	n/a
7	chr12:48382534-48382584	HRE	kidney:	n/a
8	chr12:48382534-48382584	HUVEC	blood vessel:	n/a
9	chr12:48382534-48382584	GM19239	blood:	n/a
10	chr12:48382534-48382584	RPTEC	kidney:	n/a
11	chr12:48382534-48382584	NHDF-neo	bronchial:	n/a
12	chr12:48382534-48382584	H1-hESC	embryonic stem cell:	embryo
13	chr12:48382534-48382584	HCPEpiC	choroid plexus:	n/a
14	chr12:48382534-48382584	GM06990	blood:	n/a
15	chr12:48382534-48382584	AG04450	lung:	fetal
16	chr12:48382534-48382584	HCM	heart:	n/a
17	chr12:48382534-48382584	ECC-1	luminal epithelium:	n/a
18	chr12:48382534-48382584	HMEC	breast:	n/a
19	chr12:48382534-48382584	GM12891	blood:	n/a
20	chr12:48382534-48382584	SAEC	small airway:	n/a
21	chr12:48382534-48382584	NHBE	bronchial:	n/a
22	chr12:48382534-48382584	HAEpiC	amniotic membrane:	n/a
23	chr12:48382534-48382584	HIPEpiC	eye:	n/a
24	chr12:48382534-48382584	HEK293	kidney:	embryo
25	chr12:48382534-48382584	U87	brain:	n/a
26	chr12:48382534-48382584	HNPCEpiC	eye:	n/a
27	chr12:48382534-48382584	SK-N-MC	brain:	n/a
28	chr12:48382534-48382584	NT2-D1	testis:	n/a
29	chr12:48382534-48382584	Jurkat	blood:	n/a
30	chr12:48382534-48382584	HepG2	liver:	n/a
31	chr12:48382534-48382584	A549	lung:	n/a
32	chr12:48382534-48382584	MCF-7	breast:	n/a
33	chr12:48382534-48382584	PrEC	prostate:	n/a
34	chr12:48382534-48382584	ProgFib	skin:	n/a
35	chr12:48382534-48382584	CMK	blood:	n/a
36	chr12:48382534-48382584	SKMC	muscle:	n/a
37	chr12:48382534-48382584	HL-60	blood:	n/a
38	chr12:48382534-48382584	GM12878	blood:	n/a
39	chr12:48382534-48382584	NB4	blood:	n/a
40	chr12:48382534-48382584	SK-N-SH_RA	brain:	n/a
41	chr12:48382534-48382584	PANC-1	pancreas:	n/a
42	chr12:48382534-48382584	MCF10A-Er-Src	breast:	n/a
43	chr12:48382534-48382584	HRPEpiC	eye:	n/a
44	chr12:48382534-48382584	GM12892	blood:	n/a
45	chr12:48382534-48382584	AG09309	skin:	n/a
46	chr12:48382534-48382584	T-47D	breast:	n/a
47	chr12:48382534-48382584	AG09319	gingival:	n/a
48	chr12:48382534-48382584	HRCEpiC	kidney:	n/a
49	chr12:48382534-48382584	HEEpiC	esophagus:	n/a
50	chr12:48382534-48382584	Caco-2	colon:	n/a

No data

Variant related genes	Relation type
COL2A1	TF binding region
COL2A1	CpG island

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10875716	0.95[EUR][1000 genomes]
rs10875721	0.80[EUR][1000 genomes]
rs11168338	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11168343	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11168351	0.87[EUR][1000 genomes]
rs12811832	0.83[EUR][1000 genomes]
rs7971880	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv899061	chr12:48360620-48389023	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv519659	chr12:48366449-48389245	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12817104	H1FNT	cis	Muscle Skeletal	GTEx
rs12817104	KCTD4	trans	lymphoblastoid	RTeQTL
rs12817104	RP1-228P16.1	cis	Artery Tibial	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48359200-48384000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr12:48363400-48383000	Weak transcription	Spleen	Spleen
3	chr12:48376800-48391000	Weak transcription	Fetal Intestine Large	intestine
4	chr12:48381000-48383600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr12:48381200-48382600	Enhancers	Fetal Brain Male	brain
6	chr12:48381200-48385400	Enhancers	Fetal Muscle Leg	muscle
7	chr12:48381200-48385800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:48381400-48382600	Bivalent Enhancer	Fetal Stomach	stomach
9	chr12:48381400-48383800	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:48381400-48384400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr12:48381400-48386400	Enhancers	Primary B cells from peripheral blood	blood
12	chr12:48381400-48386800	Genic enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:48381400-48388800	Weak transcription	Fetal Intestine Small	intestine
14	chr12:48381600-48382600	Enhancers	Fetal Brain Female	brain
15	chr12:48381600-48383000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
16	chr12:48381600-48383200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:48381600-48383200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr12:48381800-48382600	Enhancers	Adipose Nuclei	Adipose
19	chr12:48381800-48382800	Enhancers	H1 Cell Line	embryonic stem cell
20	chr12:48381800-48382800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr12:48381800-48383000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
22	chr12:48381800-48383000	Weak transcription	Fetal Thymus	thymus
23	chr12:48381800-48383800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr12:48381800-48383800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr12:48381800-48383800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
26	chr12:48382000-48382600	Enhancers	iPS-18 Cell Line	embryonic stem cell
27	chr12:48382000-48382600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
28	chr12:48382000-48382600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr12:48382000-48382800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr12:48382000-48383000	Enhancers	Brain Germinal Matrix	brain
31	chr12:48382000-48383200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr12:48382200-48382600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr12:48382200-48382600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr12:48382200-48383000	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr12:48382200-48383200	Weak transcription	Primary B cells from cord blood	blood
36	chr12:48382200-48385000	Weak transcription	Right Atrium	heart
37	chr12:48382400-48382600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr12:48382400-48382800	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr12:48382400-48383200	Enhancers	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links