Variant report

Variant	rs9823697
Chromosome Location	chr3:53002150-53002151
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11130331	0.84[CEU][hapmap]
rs11708223	0.80[ASN][1000 genomes]
rs11922975	0.88[ASW][hapmap];0.80[CEU][hapmap];0.87[LWK][hapmap];0.87[MKK][hapmap];0.93[YRI][hapmap]
rs2245424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2246556	0.91[CHB][hapmap];0.86[GIH][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2255107	0.86[JPT][hapmap]
rs2257216	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2336669	0.91[JPT][hapmap]
rs2336670	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2336672	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2439434	0.95[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2465101	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2564930	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2564947	0.86[JPT][hapmap]
rs2581780	0.86[JPT][hapmap]
rs2581801	0.86[JPT][hapmap]
rs2581803	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2581805	0.80[ASN][1000 genomes]
rs2581810	0.91[JPT][hapmap]
rs2581815	0.91[JPT][hapmap]
rs2581816	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2581819	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2581827	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2710313	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2710314	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2710326	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2710339	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2710345	0.80[ASN][1000 genomes]
rs2710346	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3821873	0.85[YRI][hapmap]
rs4515041	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4519686	0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs4687687	0.80[CEU][hapmap]
rs6445550	0.82[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs6768844	0.91[JPT][hapmap]
rs6770957	0.80[ASN][1000 genomes]
rs6771610	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs6792578	0.91[JPT][hapmap]
rs6795646	0.90[GIH][hapmap];0.82[YRI][hapmap]
rs6799185	1.00[CEU][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs6801235	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7626551	0.80[CEU][hapmap];0.93[YRI][hapmap]
rs7648514	0.89[JPT][hapmap]
rs9311485	0.91[JPT][hapmap]
rs9810807	0.85[YRI][hapmap]
rs9828491	0.80[ASN][1000 genomes]
rs9846976	0.91[JPT][hapmap]
rs9860296	0.90[GIH][hapmap];0.82[YRI][hapmap]
rs9865094	0.91[JPT][hapmap]
rs9985365	0.84[CEU][hapmap]

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	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv1818974	chr3:52966316-53096394	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs9823697	SEMA3G	cis	parietal	SCAN
rs9823697	TEX264	cis	parietal	SCAN
rs9823697	ITIH4-AS1	cis	Artery Aorta	GTEx
rs9823697	ITIH4	cis	cerebellum	SCAN
rs9823697	GNL3	cis	parietal	SCAN
rs9823697	ITIH4-AS1	cis	lung	GTEx
rs9823697	ITIH4-AS1	cis	Artery Tibial	GTEx
rs9823697	ITIH4	cis	lymphoblastoid	seeQTL
rs9823697	SFMBT1	cis	cerebellum	SCAN
rs9823697	ITIH4	cis	parietal	SCAN
rs9823697	GNL3	cis	cerebellum	SCAN
rs9823697	GLT8D1	cis	brain	seeQTL

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52954000-53012200	Weak transcription	Esophagus	oesophagus
2	chr3:52954200-53012200	Weak transcription	Pancreas	Pancrea
3	chr3:52962400-53007000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr3:52962400-53012400	Weak transcription	Adipose Nuclei	Adipose
5	chr3:52964600-53012200	Weak transcription	Fetal Muscle Leg	muscle
6	chr3:52965000-53039800	Weak transcription	Left Ventricle	heart
7	chr3:52965600-53008200	Weak transcription	GM12878-XiMat	blood
8	chr3:52969000-53008000	Weak transcription	Colon Smooth Muscle	Colon
9	chr3:52975000-53008000	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr3:52977600-53017000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr3:52984400-53006000	Weak transcription	Fetal Heart	heart
12	chr3:52984600-53003000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr3:52986400-53012200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:52986800-53006200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr3:52987000-53003200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr3:52987200-53017400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr3:52987400-53002800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr3:52987400-53004600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr3:52987600-53003600	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr3:52987600-53005800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr3:52987600-53009400	Weak transcription	Placenta	Placenta
22	chr3:52987600-53014200	Weak transcription	Fetal Thymus	thymus
23	chr3:52987600-53014200	Weak transcription	Thymus	Thymus
24	chr3:52987800-53004600	Weak transcription	Fetal Muscle Trunk	muscle
25	chr3:52987800-53017000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr3:52987800-53017000	Weak transcription	Monocytes-CD14+_RO01746	blood
27	chr3:52988000-53003000	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr3:52988000-53004800	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr3:52988000-53014200	Weak transcription	Primary T cells from cord blood	blood
30	chr3:52992000-53003400	Weak transcription	Primary B cells from peripheral blood	blood
31	chr3:52992000-53015800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr3:52992200-53005600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr3:52992800-53002600	Weak transcription	Ovary	ovary
34	chr3:52993800-53016800	Weak transcription	Primary B cells from cord blood	blood
35	chr3:52995200-53007000	Weak transcription	Right Ventricle	heart
36	chr3:52996600-53002800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr3:52997200-53008200	Weak transcription	A549	lung
38	chr3:52998600-53004400	Weak transcription	Fetal Stomach	stomach
39	chr3:52998800-53002600	Weak transcription	Fetal Intestine Small	intestine
40	chr3:52998800-53002800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr3:52999000-53008200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr3:52999600-53002200	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr3:52999800-53003200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr3:53000600-53002400	Strong transcription	Hela-S3	cervix
45	chr3:53000800-53003400	Strong transcription	Dnd41	blood
46	chr3:53001200-53003600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:53001400-53002600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr3:53001400-53003400	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr3:53001400-53008000	Weak transcription	Osteobl	bone
50	chr3:53001600-53002200	Strong transcription	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links