Variant report

Variant	rs9567962
Chromosome Location	chr13:48537289-48537290
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12427964	0.82[ASN][1000 genomes]
rs12429993	0.94[ASN][1000 genomes]
rs12431057	0.82[ASN][1000 genomes]
rs2148242	0.82[ASN][1000 genomes]
rs2182219	0.83[AMR][1000 genomes]
rs2182374	0.82[ASN][1000 genomes]
rs2182375	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2182377	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2897496	0.82[ASN][1000 genomes]
rs4942741	0.94[EUR][1000 genomes]
rs7325115	0.83[AMR][1000 genomes]
rs7336631	0.94[EUR][1000 genomes]
rs7982479	0.95[EUR][1000 genomes]
rs7987109	0.83[AMR][1000 genomes]
rs7988917	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7997347	0.94[EUR][1000 genomes]
rs8002322	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs840430	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9526440	0.94[EUR][1000 genomes]
rs9534910	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9534936	0.93[AMR][1000 genomes];0.95[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9567962	MED4	cis	multi-tissue	Pritchard
rs9567962	MED4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48507200-48548800	Weak transcription	Stomach Mucosa	stomach
2	chr13:48512600-48537600	Weak transcription	Hela-S3	cervix
3	chr13:48514400-48574000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr13:48523000-48541600	Weak transcription	Psoas Muscle	Psoas
5	chr13:48523000-48542600	Weak transcription	K562	blood
6	chr13:48528000-48545800	Weak transcription	Colon Smooth Muscle	Colon
7	chr13:48528600-48541000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr13:48529400-48540200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
9	chr13:48530000-48538400	ZNF genes & repeats	Dnd41	blood
10	chr13:48530000-48541000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr13:48530000-48541200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
12	chr13:48530600-48538400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
13	chr13:48530600-48538800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
14	chr13:48530600-48540200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr13:48530600-48540400	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
16	chr13:48532000-48540800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr13:48532000-48551400	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr13:48532200-48565200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr13:48532400-48539800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr13:48532400-48540600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr13:48532400-48546000	Weak transcription	Aorta	Aorta
22	chr13:48532400-48559400	Weak transcription	Gastric	stomach
23	chr13:48532400-48565200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr13:48532600-48545800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr13:48532800-48545800	Weak transcription	Brain Substantia Nigra	brain
26	chr13:48533200-48540600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr13:48533600-48539400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr13:48533600-48540200	Strong transcription	Placenta	Placenta
29	chr13:48533800-48548000	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr13:48534000-48538400	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr13:48534000-48540400	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
32	chr13:48534000-48541200	Strong transcription	Fetal Thymus	thymus
33	chr13:48534000-48543000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr13:48534000-48560800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr13:48534200-48537800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr13:48534200-48538000	Weak transcription	NH-A	brain
37	chr13:48534200-48538600	Strong transcription	Fetal Kidney	kidney
38	chr13:48534200-48540400	Strong transcription	Primary T cells from cord blood	blood
39	chr13:48534200-48540600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr13:48534200-48540600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr13:48534200-48540600	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr13:48534200-48541400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr13:48534200-48541600	Weak transcription	Rectal Smooth Muscle	rectum
44	chr13:48534200-48542800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr13:48534200-48542800	Strong transcription	Adipose Nuclei	Adipose
46	chr13:48534200-48543000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr13:48534200-48545200	Weak transcription	Spleen	Spleen
48	chr13:48534200-48545800	Weak transcription	Brain Cingulate Gyrus	brain
49	chr13:48534200-48573200	Weak transcription	Brain Angular Gyrus	brain
50	chr13:48534400-48538000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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