Variant report

Variant	rs12637699
Chromosome Location	chr3:46628443-46628444
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1049667	1.00[YRI][hapmap]
rs11705987	0.87[MEX][hapmap]
rs11718490	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11718494	0.96[ASN][1000 genomes]
rs13098842	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17220622	0.87[MEX][hapmap]
rs3806701	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3806702	0.82[CEU][hapmap];0.81[GIH][hapmap];0.87[MEX][hapmap];0.85[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4682823	0.92[EUR][1000 genomes]
rs6442006	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6442008	0.92[EUR][1000 genomes]
rs6769392	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6783573	0.86[CHB][hapmap];1.00[YRI][hapmap]
rs9682509	0.89[AMR][1000 genomes]

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	nsv1013306	chr3:46469014-46698538	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs12637699	TDGF1	cis	Muscle Skeletal	GTEx
rs12637699	TDGF1	cis	Nerve Tibial	GTEx
rs12637699	P4HTM	cis	parietal	SCAN
rs12637699	LRRC2	cis	cerebellum	SCAN
rs12637699	TDGF1	cis	Esophagus Muscularis	GTEx
rs12637699	ABHD5	cis	parietal	SCAN
rs12637699	CCDC71	cis	cerebellum	SCAN
rs12637699	MAP4	cis	parietal	SCAN
rs12637699	TDGF1	cis	parietal	SCAN
rs12637699	TDGF1	cis	Heart Left Ventricle	GTEx
rs12637699	TDGF1	cis	cerebellum	SCAN
rs12637699	TDGF1	cis	Adipose Subcutaneous	GTEx
rs12637699	HYAL3	cis	parietal	SCAN
rs12637699	SLC38A3	cis	cerebellum	SCAN
rs12637699	TDGF1	cis	lung	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46624000-46628800	Enhancers	Liver	Liver
2	chr3:46624400-46628800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
3	chr3:46625400-46628800	Strong transcription	Right Atrium	heart
4	chr3:46626200-46630200	Enhancers	Dnd41	blood
5	chr3:46626400-46629200	Enhancers	Stomach Mucosa	stomach
6	chr3:46626600-46628600	Enhancers	Colonic Mucosa	Colon
7	chr3:46626600-46628800	Enhancers	Pancreas	Pancrea
8	chr3:46626800-46628600	Enhancers	Rectal Mucosa Donor 29	rectum
9	chr3:46626800-46628800	Enhancers	Fetal Intestine Large	intestine
10	chr3:46626800-46629000	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr3:46627000-46628600	Enhancers	Fetal Intestine Small	intestine
12	chr3:46627000-46629200	Enhancers	Fetal Thymus	thymus
13	chr3:46627200-46628800	Enhancers	Duodenum Mucosa	Duodenum
14	chr3:46627200-46634600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:46627200-46637000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:46627600-46628800	Enhancers	Primary T cells from cord blood	blood
17	chr3:46627800-46629800	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr3:46628200-46628600	Enhancers	Gastric	stomach
19	chr3:46628200-46628800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
20	chr3:46628200-46628800	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr3:46628200-46628800	Enhancers	Small Intestine	intestine
22	chr3:46628200-46629000	Enhancers	Thymus	Thymus
23	chr3:46628200-46629200	Enhancers	HepG2	liver
24	chr3:46628400-46628600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
25	chr3:46628400-46628800	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr3:46628400-46631000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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