Variant report

Variant	rs8002322
Chromosome Location	chr13:48549906-48549907
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs12427516	0.82[ASN][1000 genomes]
rs12427964	0.94[ASN][1000 genomes]
rs12428055	0.82[ASN][1000 genomes]
rs12428102	0.82[ASN][1000 genomes]
rs12429099	0.82[ASN][1000 genomes]
rs12429348	0.82[ASN][1000 genomes]
rs12429746	0.82[ASN][1000 genomes]
rs12429993	0.82[ASN][1000 genomes]
rs12430076	0.82[ASN][1000 genomes]
rs12431057	0.94[ASN][1000 genomes]
rs17071168	0.86[TSI][hapmap]
rs1968029	0.82[ASN][1000 genomes]
rs2094191	0.82[ASN][1000 genomes]
rs2094196	0.81[MEX][hapmap]
rs2148242	0.94[ASN][1000 genomes]
rs2182219	0.83[AMR][1000 genomes]
rs2182374	0.94[ASN][1000 genomes]
rs2182375	0.86[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2182377	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2897496	0.94[ASN][1000 genomes]
rs35710390	0.82[ASN][1000 genomes]
rs4941618	1.00[MEX][hapmap]
rs4942741	0.94[EUR][1000 genomes]
rs57698455	0.82[ASN][1000 genomes]
rs57957392	0.82[ASN][1000 genomes]
rs58634823	0.82[ASN][1000 genomes]
rs61585711	0.82[ASN][1000 genomes]
rs7323702	0.90[MEX][hapmap]
rs7325115	0.83[AMR][1000 genomes]
rs7332363	0.90[MEX][hapmap]
rs7332994	0.90[MEX][hapmap]
rs7335797	1.00[MEX][hapmap]
rs7336631	0.94[EUR][1000 genomes]
rs7982479	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs7987109	0.83[AMR][1000 genomes]
rs7988917	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7990099	0.90[MEX][hapmap]
rs7991892	1.00[MEX][hapmap]
rs7996581	0.90[MEX][hapmap]
rs7997347	0.88[CEU][hapmap];0.83[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs840430	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526440	0.94[EUR][1000 genomes]
rs9526455	0.90[MEX][hapmap]
rs9534910	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534936	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9534966	0.90[MEX][hapmap]
rs9567962	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][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	nsv933980	chr13:48431000-48557419	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs8002322	MED4	cis	multi-tissue	Pritchard
rs8002322	FAM194B	cis	cerebellum	SCAN
rs8002322	MED4	cis	normal skin	skin_eQTL
rs8002322	MED4	cis	parietal	SCAN
rs8002322	MED4	Cis_1M	lymphoblastoid	RTeQTL
rs8002322	MED4	cis	uninvolved skin	skin_eQTL
rs8002322	MED4	cis	lesional skin	skin_eQTL
rs8002322	MED4	cis	cerebellum	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48514400-48574000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr13:48532000-48551400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr13:48532200-48565200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr13:48532400-48559400	Weak transcription	Gastric	stomach
5	chr13:48532400-48565200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr13:48534000-48560800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr13:48534200-48573200	Weak transcription	Brain Angular Gyrus	brain
8	chr13:48534400-48574400	Weak transcription	Small Intestine	intestine
9	chr13:48534600-48550400	Weak transcription	Right Ventricle	heart
10	chr13:48535000-48564800	Weak transcription	NHLF	lung
11	chr13:48535200-48552000	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr13:48536000-48550400	Weak transcription	Fetal Heart	heart
13	chr13:48536200-48550000	Weak transcription	NHEK	skin
14	chr13:48537200-48574200	Weak transcription	Colonic Mucosa	Colon
15	chr13:48537400-48560200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr13:48537400-48574000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr13:48537400-48574400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr13:48538000-48567200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr13:48538400-48551000	Weak transcription	Fetal Brain Male	brain
20	chr13:48538400-48551600	Weak transcription	Brain Hippocampus Middle	brain
21	chr13:48538400-48574000	Weak transcription	Hela-S3	cervix
22	chr13:48538600-48559800	Weak transcription	HUVEC	blood vessel
23	chr13:48538800-48564800	Weak transcription	Brain Germinal Matrix	brain
24	chr13:48539400-48551800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr13:48539600-48571200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr13:48540000-48574200	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr13:48540200-48552600	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr13:48540200-48559000	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr13:48540600-48550000	Weak transcription	HSMMtube	muscle
30	chr13:48540800-48565000	Weak transcription	NH-A	brain
31	chr13:48541800-48550000	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr13:48542000-48558800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr13:48542400-48551600	Weak transcription	HMEC	breast
34	chr13:48542400-48564800	Weak transcription	Rectal Smooth Muscle	rectum
35	chr13:48542400-48565200	Weak transcription	Psoas Muscle	Psoas
36	chr13:48542400-48567000	Weak transcription	Esophagus	oesophagus
37	chr13:48542800-48553800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr13:48542800-48559000	Weak transcription	HSMM	muscle
39	chr13:48543000-48553600	Weak transcription	Fetal Kidney	kidney
40	chr13:48543000-48574400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr13:48543400-48560600	Weak transcription	HepG2	liver
42	chr13:48544000-48550400	Weak transcription	GM12878-XiMat	blood
43	chr13:48544000-48551400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr13:48545000-48550800	Strong transcription	Fetal Muscle Trunk	muscle
45	chr13:48545200-48551400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr13:48545200-48551600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr13:48546200-48551600	Weak transcription	A549	lung
48	chr13:48546400-48559400	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr13:48546400-48564600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr13:48546400-48565200	Weak transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links