Variant report

Variant	rs2970049
Chromosome Location	chr17:50236610-50236611
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3A	chr17:50235229-50236733	H1-hESC	embryonic stem cell:	n/a	chr17:50236213-50236226
2	CTBP2	chr17:50235074-50237787	H1-hESC	embryonic stem cell:	n/a	n/a
3	ZNF263	chr17:50235690-50236902	HEK293-T-REx	kidney:	n/a	chr17:50236301-50236310 chr17:50236292-50236301 chr17:50236295-50236304 chr17:50236290-50236311 chr17:50236698-50236707 chr17:50236298-50236307

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr17:50236572-50236622	PrEC	prostate:	n/a
2	chr17:50236572-50236622	SK-N-SH	brain:	n/a
3	chr17:50236572-50236622	HCM	heart:	n/a
4	chr17:50236572-50236622	ECC-1	luminal epithelium:	n/a
5	chr17:50236572-50236622	GM12892	blood:	n/a
6	chr17:50236572-50236622	HCT-116	colon:	n/a
7	chr17:50236572-50236622	HNPCEpiC	eye:	n/a
8	chr17:50236572-50236622	RPTEC	kidney:	n/a
9	chr17:50236572-50236622	SKMC	muscle:	n/a
10	chr17:50236572-50236622	H1-hESC	embryonic stem cell:	embryo
11	chr17:50236572-50236622	ProgFib	skin:	n/a
12	chr17:50236572-50236622	LNCaP	prostate:	n/a
13	chr17:50236572-50236622	HepG2	liver:	n/a
14	chr17:50236572-50236622	PANC-1	pancreas:	n/a
15	chr17:50236572-50236622	A549	lung:	n/a
16	chr17:50236572-50236622	IMR90	lung:	fetal
17	chr17:50236572-50236622	BJ	skin:	n/a
18	chr17:50236572-50236622	HRE	kidney:	n/a
19	chr17:50236572-50236622	HCPEpiC	choroid plexus:	n/a
20	chr17:50236572-50236622	Hepatocyte	liver:	n/a
21	chr17:50236572-50236622	NHBE	bronchial:	n/a
22	chr17:50236572-50236622	AG04450	lung:	fetal
23	chr17:50236572-50236622	T-47D	breast:	n/a
24	chr17:50236572-50236622	GM12878	blood:	n/a
25	chr17:50236572-50236622	SAEC	small airway:	n/a
26	chr17:50236572-50236622	HUVEC	blood vessel:	n/a
27	chr17:50236572-50236622	K562	blood:	n/a
28	chr17:50236572-50236622	U87	brain:	n/a
29	chr17:50236572-50236622	HAEpiC	amniotic membrane:	n/a
30	chr17:50236572-50236622	HPAEpiC	pulmonary alveolar:	n/a
31	chr17:50236572-50236622	Jurkat	blood:	n/a
32	chr17:50236572-50236622	SK-N-MC	brain:	n/a
33	chr17:50236572-50236622	HMEC	breast:	n/a
34	chr17:50236572-50236622	Caco-2	colon:	n/a
35	chr17:50236572-50236622	HEEpiC	esophagus:	n/a
36	chr17:50236572-50236622	HCF	heart:	n/a
37	chr17:50236572-50236622	SK-N-SH_RA	brain:	n/a
38	chr17:50236572-50236622	AG09309	skin:	n/a
39	chr17:50236572-50236622	AG04449	skin:	fetal
40	chr17:50236572-50236622	Hela-S3	cervix:	n/a
41	chr17:50236572-50236622	HEK293	kidney:	embryo
42	chr17:50236572-50236622	HL-60	blood:	n/a
43	chr17:50236572-50236622	GM19239	blood:	n/a
44	chr17:50236572-50236622	BE2_C	brain:	n/a
45	chr17:50236572-50236622	HIPEpiC	eye:	n/a
46	chr17:50236572-50236622	CMK	blood:	n/a
47	chr17:50236572-50236622	GM12891	blood:	n/a
48	chr17:50236572-50236622	AoSMC	blood vessel:	n/a
49	chr17:50236572-50236622	HRPEpiC	eye:	n/a
50	chr17:50236572-50236622	NH-A	brain:	n/a

No data

Variant related genes	Relation type
CA10	TF binding region
CA10	CpG island

Extended variants
information (count: 10 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12600466	0.86[JPT][hapmap]
rs12950144	0.86[JPT][hapmap]
rs12950394	0.86[JPT][hapmap]
rs1393730	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1503045	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1503046	1.00[CEU][hapmap];0.93[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2036483	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2970052	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8076676	0.86[JPT][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	nsv492317	chr17:50067819-50774475	Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2970049	ZNF652	cis	cerebellum	SCAN
rs2970049	MYL4	cis	parietal	SCAN
rs2970049	CDC27	cis	parietal	SCAN
rs2970049	HOXB13	cis	parietal	SCAN
rs2970049	CACNA1G	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:50233800-50237800	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
2	chr17:50234200-50237800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
3	chr17:50234400-50238000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
4	chr17:50234600-50237400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
5	chr17:50234600-50237800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr17:50234600-50238000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
7	chr17:50234600-50238000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
8	chr17:50234800-50236800	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
9	chr17:50234800-50237800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr17:50235000-50236800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr17:50235000-50237800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
12	chr17:50235000-50237800	Bivalent/Poised TSS	Brain Substantia Nigra	brain
13	chr17:50235200-50236800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr17:50235200-50236800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr17:50235200-50237000	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
16	chr17:50235200-50237200	Enhancers	Pancreas	Pancrea
17	chr17:50235400-50236800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
18	chr17:50235400-50237200	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr17:50235400-50237600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
20	chr17:50235400-50237600	ZNF genes & repeats	Spleen	Spleen
21	chr17:50235400-50237800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
22	chr17:50235800-50236800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr17:50235800-50237000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr17:50235800-50237800	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
25	chr17:50236000-50236800	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
26	chr17:50236000-50236800	Bivalent Enhancer	Fetal Muscle Leg	muscle
27	chr17:50236000-50237000	Bivalent/Poised TSS	Brain Anterior Caudate	brain
28	chr17:50236200-50236800	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
29	chr17:50236400-50236800	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
30	chr17:50236400-50236800	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
31	chr17:50236400-50237000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr17:50236400-50237400	Flanking Bivalent TSS/Enh	NHEK	skin
33	chr17:50236600-50236800	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr17:50236600-50236800	Flanking Bivalent TSS/Enh	Brain Dorsolateral Prefrontal Cortex	brain
35	chr17:50236600-50236800	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
36	chr17:50236600-50236800	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
37	chr17:50236600-50236800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
38	chr17:50236600-50236800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
39	chr17:50236600-50237000	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr17:50236600-50237000	Bivalent Enhancer	HMEC	breast
41	chr17:50236600-50237400	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
42	chr17:50236600-50237800	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
43	chr17:50236600-50238000	Bivalent/Poised TSS	Brain Angular Gyrus	brain

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