Variant report

Variant	rs9316349
Chromosome Location	chr13:48666828-48666829
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs12584652	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1327655	0.84[EUR][1000 genomes]
rs17350996	1.00[CEU][hapmap];0.80[JPT][hapmap];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17425881	1.00[CEU][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap]
rs2025865	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2296573	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs35299472	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3809330	0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4941627	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4942742	0.81[EUR][1000 genomes]
rs4942743	0.88[EUR][1000 genomes]
rs4942747	0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs4942749	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4942750	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs4942751	0.88[EUR][1000 genomes]
rs4942752	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6561434	0.88[EUR][1000 genomes]
rs7317431	0.84[EUR][1000 genomes]
rs7317860	0.91[JPT][hapmap]
rs7318704	0.84[EUR][1000 genomes]
rs7322766	0.84[EUR][1000 genomes]
rs7323969	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7330472	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7331900	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7332326	0.87[EUR][1000 genomes]
rs7333247	0.83[EUR][1000 genomes]
rs7334463	0.85[JPT][hapmap]
rs7338844	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7338999	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7339370	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7981114	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7986400	0.88[EUR][1000 genomes]
rs7990060	0.88[EUR][1000 genomes]
rs9285165	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9316346	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9316347	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9316348	0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs9316352	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs9316353	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9316354	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9316355	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9316356	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9316357	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9316358	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9316359	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9316360	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9562800	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9562806	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9562808	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9567979	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9567993	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9567999	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9568000	0.84[EUR][1000 genomes]
rs9568001	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9568002	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9568003	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9568004	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9568005	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9568006	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9568008	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9568009	0.87[EUR][1000 genomes]
rs9568010	0.84[EUR][1000 genomes]
rs9568015	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9591135	0.88[EUR][1000 genomes]
rs9591138	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9591139	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9591140	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9595835	0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs9595836	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9595837	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9595843	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9595852	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430556	chr13:48516799-48679099	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv832601	chr13:48569952-48735939	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9316349	MED4	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48648600-48667400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr13:48652800-48668200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr13:48653000-48667800	Weak transcription	Stomach Mucosa	stomach
4	chr13:48653000-48668200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr13:48653200-48668200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr13:48653800-48667600	Weak transcription	A549	lung
7	chr13:48654200-48667600	Weak transcription	Right Ventricle	heart
8	chr13:48655400-48667000	Weak transcription	Gastric	stomach
9	chr13:48655400-48667600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr13:48655400-48668000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr13:48655400-48668200	Weak transcription	Aorta	Aorta
12	chr13:48656200-48667000	Weak transcription	HUVEC	blood vessel
13	chr13:48656200-48668000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr13:48657400-48667600	Weak transcription	Brain Angular Gyrus	brain
15	chr13:48657400-48668000	Weak transcription	HSMMtube	muscle
16	chr13:48657600-48667000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr13:48657600-48667600	Weak transcription	Brain Substantia Nigra	brain
18	chr13:48657800-48667200	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr13:48658000-48667000	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr13:48658000-48667000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr13:48658000-48667200	Weak transcription	NH-A	brain
22	chr13:48658000-48667600	Weak transcription	Colonic Mucosa	Colon
23	chr13:48658200-48667800	Weak transcription	Brain Cingulate Gyrus	brain
24	chr13:48658400-48667000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr13:48658800-48667600	Weak transcription	Brain Hippocampus Middle	brain
26	chr13:48658800-48667600	Weak transcription	Fetal Brain Male	brain
27	chr13:48658800-48667600	Weak transcription	Fetal Lung	lung
28	chr13:48659000-48667800	Weak transcription	Fetal Kidney	kidney
29	chr13:48659400-48667800	Weak transcription	Brain Germinal Matrix	brain
30	chr13:48659600-48667600	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr13:48659600-48668000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr13:48659800-48667000	Weak transcription	Brain Anterior Caudate	brain
33	chr13:48659800-48667000	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr13:48659800-48667000	Weak transcription	Thymus	Thymus
35	chr13:48659800-48667600	Weak transcription	Fetal Stomach	stomach
36	chr13:48659800-48667600	Weak transcription	Ovary	ovary
37	chr13:48659800-48667800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr13:48659800-48668200	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr13:48660000-48667400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr13:48660000-48667600	Weak transcription	Fetal Intestine Large	intestine
41	chr13:48660400-48667000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr13:48660400-48667000	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr13:48660400-48667600	Weak transcription	NHLF	lung
44	chr13:48660400-48667800	Weak transcription	Placenta	Placenta
45	chr13:48660600-48667000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr13:48660600-48667000	Weak transcription	Fetal Thymus	thymus
47	chr13:48660600-48667000	Weak transcription	HMEC	breast
48	chr13:48660600-48667200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr13:48660600-48667200	Weak transcription	Osteobl	bone
50	chr13:48660600-48667400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links