Variant report

Variant	rs4974078
Chromosome Location	chr3:49009386-49009387
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:48997273..48999168-chr3:49008548..49010933,2	K562	blood:

Extended variants
information (count: 100 )
Associated
traits (count: 31 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10780033	0.85[CHB][hapmap];0.87[CHD][hapmap];0.88[ASN][1000 genomes]
rs11130176	0.85[CHB][hapmap];0.87[CHD][hapmap];0.88[ASN][1000 genomes]
rs1134591	0.88[ASN][1000 genomes]
rs11705737	0.88[ASN][1000 genomes]
rs11706052	0.87[CHD][hapmap]
rs11709246	0.88[ASN][1000 genomes]
rs11712982	0.85[ASN][1000 genomes]
rs11713694	0.87[CHD][hapmap];0.80[ASN][1000 genomes]
rs11715581	1.00[CHD][hapmap]
rs11717978	0.88[ASN][1000 genomes]
rs11719457	0.88[ASN][1000 genomes]
rs11920534	0.85[CHB][hapmap];0.87[CHD][hapmap];0.90[ASN][1000 genomes]
rs11924597	0.90[ASN][1000 genomes]
rs12490393	1.00[CHD][hapmap]
rs12493001	0.87[CHD][hapmap]
rs12493289	0.83[ASN][1000 genomes]
rs13064911	0.88[ASN][1000 genomes]
rs13072911	0.88[ASN][1000 genomes]
rs13073997	0.83[ASN][1000 genomes]
rs13086240	0.90[ASN][1000 genomes]
rs13087930	0.87[CHD][hapmap];0.88[ASN][1000 genomes]
rs13090839	0.85[ASN][1000 genomes]
rs13092715	0.85[CHB][hapmap]
rs13094900	0.80[ASN][1000 genomes]
rs13315711	0.85[CHB][hapmap];0.93[ASN][1000 genomes]
rs13316620	0.80[ASN][1000 genomes]
rs28642807	0.83[ASN][1000 genomes]
rs3212	0.85[CHB][hapmap];0.87[CHD][hapmap]
rs34037363	0.87[CHD][hapmap]
rs34477108	0.88[ASN][1000 genomes]
rs34504524	0.85[ASN][1000 genomes]
rs34509487	0.88[ASN][1000 genomes]
rs35283189	0.87[CHD][hapmap]
rs35673421	0.87[CHD][hapmap]
rs4072859	0.85[ASN][1000 genomes]
rs4279134	0.85[CHB][hapmap];0.87[CHD][hapmap]
rs4513485	0.85[CHB][hapmap];0.87[CHD][hapmap]
rs4521268	0.85[CHB][hapmap];0.87[CHD][hapmap]
rs4955410	0.87[CHD][hapmap]
rs4955418	1.00[CHD][hapmap]
rs4955420	1.00[CHD][hapmap]
rs4974079	0.87[CHD][hapmap];0.83[ASN][1000 genomes]
rs4974080	0.85[CHB][hapmap];0.87[CHD][hapmap];0.90[ASN][1000 genomes]
rs4974082	0.85[CHB][hapmap];0.87[CHD][hapmap];0.95[ASN][1000 genomes]
rs4974084	0.90[ASN][1000 genomes]
rs4974085	0.85[CHB][hapmap];0.87[CHD][hapmap];0.88[ASN][1000 genomes]
rs4974087	0.87[CHD][hapmap];0.88[ASN][1000 genomes]
rs5030795	0.87[CHD][hapmap]
rs55674449	0.81[ASN][1000 genomes]
rs56318350	0.88[ASN][1000 genomes]
rs6414613	0.85[CHB][hapmap];0.87[CHD][hapmap];0.90[ASN][1000 genomes]
rs6446196	0.90[ASN][1000 genomes]
rs6446198	0.88[ASN][1000 genomes]
rs6446205	0.85[CHB][hapmap];0.87[CHD][hapmap];0.90[ASN][1000 genomes]
rs6446252	0.88[ASN][1000 genomes]
rs6446253	0.83[ASN][1000 genomes]
rs67060340	0.83[ASN][1000 genomes]
rs67332931	0.88[ASN][1000 genomes]
rs6768433	0.82[CEU][hapmap];0.84[ASN][1000 genomes]
rs6781790	0.85[CHB][hapmap];0.87[CHD][hapmap];0.90[ASN][1000 genomes]
rs6786665	0.93[ASN][1000 genomes]
rs6791234	0.88[ASN][1000 genomes]
rs71324924	0.88[ASN][1000 genomes]
rs7373778	0.80[ASN][1000 genomes]
rs7430198	0.87[CHD][hapmap];0.88[ASN][1000 genomes]
rs7430501	0.85[CHB][hapmap];0.87[CHD][hapmap];0.88[ASN][1000 genomes]
rs7431710	0.85[CHB][hapmap];0.87[CHD][hapmap];0.93[ASN][1000 genomes]
rs7431857	0.85[CHB][hapmap];0.87[CHD][hapmap];0.88[ASN][1000 genomes]
rs7432989	0.87[CHD][hapmap]
rs7612459	0.83[ASN][1000 genomes]
rs7621015	0.85[CHB][hapmap];0.87[CHD][hapmap];0.80[ASN][1000 genomes]
rs7623023	0.85[CHB][hapmap];0.87[CHD][hapmap];0.88[ASN][1000 genomes]
rs7626445	0.85[CHB][hapmap];0.87[CHD][hapmap]
rs7627404	0.87[CHD][hapmap]
rs7628719	0.85[CHB][hapmap];0.87[CHD][hapmap];0.93[ASN][1000 genomes]
rs7636057	0.80[ASN][1000 genomes]
rs7639332	0.88[ASN][1000 genomes]
rs7643368	0.85[CHB][hapmap];0.87[CHD][hapmap];0.93[ASN][1000 genomes]
rs7647813	0.87[CHD][hapmap]
rs7649458	0.85[CHB][hapmap];0.87[CHD][hapmap];0.88[ASN][1000 genomes]
rs8926	0.85[ASN][1000 genomes]
rs9311430	0.85[CHB][hapmap];0.87[CHD][hapmap];0.88[ASN][1000 genomes]
rs9311433	0.85[CHB][hapmap];0.87[CHD][hapmap];0.88[ASN][1000 genomes]
rs9311434	0.85[CHB][hapmap];0.87[CHD][hapmap];0.83[ASN][1000 genomes]
rs9681717	0.83[ASN][1000 genomes]
rs9682444	0.81[ASN][1000 genomes]
rs9754878	0.81[ASN][1000 genomes]
rs9755490	0.83[ASN][1000 genomes]
rs9814987	0.87[CHD][hapmap]
rs9830636	0.88[ASN][1000 genomes]
rs9835307	0.87[CHD][hapmap];0.83[ASN][1000 genomes]
rs9840050	0.85[CHB][hapmap];0.87[CHD][hapmap]
rs9840684	0.88[ASN][1000 genomes]
rs9846123	0.85[CHB][hapmap];0.87[CHD][hapmap];0.81[ASN][1000 genomes]
rs9850134	0.85[CHB][hapmap];0.87[CHD][hapmap];0.88[ASN][1000 genomes]
rs9867373	0.88[ASN][1000 genomes]
rs9876848	0.87[CHD][hapmap];0.88[ASN][1000 genomes]
rs9879971	0.88[ASN][1000 genomes]
rs9880088	0.87[CHD][hapmap]
rs9884022	0.84[CEU][hapmap];0.88[ASN][1000 genomes]

mRNA abundance (count:31)

SNP	Gene	Cis/trans	Tissue	Source
rs4974078	WDR6	cis	cerebellum	SCAN
rs4974078	CCDC36	cis	Artery Tibial	GTEx
rs4974078	ARIH2	cis	cerebellum	SCAN
rs4974078	BSN-AS2	cis	Muscle Skeletal	GTEx
rs4974078	WDR6	cis	multi-tissue	Pritchard
rs4974078	NICN1-AS1	cis	Thyroid	GTEx
rs4974078	WDR6	cis	Whole Blood	GTEx
rs4974078	QRICH1	cis	parietal	SCAN
rs4974078	P4HTM	cis	parietal	SCAN
rs4974078	WDR6	cis	Adipose Subcutaneous	GTEx
rs4974078	NCKIPSD	cis	multi-tissue	Pritchard
rs4974078	SEMA3G	cis	cerebellum	SCAN
rs4974078	WDR6	cis	Artery Tibial	GTEx
rs4974078	NICN1	cis	multi-tissue	Pritchard
rs4974078	TLR9	cis	parietal	SCAN
rs4974078	WDR6	cis	Heart Left Ventricle	GTEx
rs4974078	GNL3	cis	cerebellum	SCAN
rs4974078	WDR6	cis	Muscle Skeletal	GTEx
rs4974078	WDR6	cis	Esophagus Mucosa	GTEx
rs4974078	WDR6	cis	lung	GTEx
rs4974078	ARIH2	cis	Thyroid	GTEx
rs4974078	DALRD3	cis	cerebellum	SCAN
rs4974078	PH-4	Cis_1M	lymphoblastoid	RTeQTL
rs4974078	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs4974078	AMT	cis	cerebellum	SCAN
rs4974078	AMT	cis	multi-tissue	Pritchard
rs4974078	AMT	cis	Thyroid	GTEx
rs4974078	WDR6	cis	Nerve Tibial	GTEx
rs4974078	CCDC71	cis	cerebellum	SCAN
rs4974078	WDR6	cis	parietal	SCAN
rs4974078	NICN1	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48988000-49011600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:48989800-49023600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr3:48990000-49024600	Strong transcription	Fetal Thymus	thymus
4	chr3:48990200-49010000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:48994200-49023800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:48994400-49023600	Strong transcription	Dnd41	blood
7	chr3:48994800-49010000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr3:48994800-49022000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr3:48997800-49009400	Weak transcription	Psoas Muscle	Psoas
10	chr3:48998800-49023400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr3:48999000-49021200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr3:48999000-49021600	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr3:48999200-49022000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr3:48999200-49022800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr3:48999400-49023600	Strong transcription	Primary T cells from cord blood	blood
16	chr3:48999400-49024400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:48999600-49021800	Strong transcription	Fetal Intestine Large	intestine
18	chr3:48999600-49024200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:48999600-49024400	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr3:48999600-49024600	Strong transcription	Fetal Stomach	stomach
21	chr3:48999600-49024800	Strong transcription	Fetal Intestine Small	intestine
22	chr3:49000000-49022800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr3:49001200-49023600	Strong transcription	HUES6 Cell Line	embryonic stem cell
24	chr3:49002000-49010000	Strong transcription	NHEK	skin
25	chr3:49002000-49023800	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr3:49002000-49024000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr3:49002000-49024000	Strong transcription	Liver	Liver
28	chr3:49002000-49024400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:49002000-49024600	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr3:49002000-49024800	Strong transcription	Fetal Muscle Trunk	muscle
31	chr3:49002200-49009600	Strong transcription	HepG2	liver
32	chr3:49002200-49023200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr3:49002200-49023200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr3:49002200-49023400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr3:49002200-49023800	Strong transcription	HUES48 Cell Line	embryonic stem cell
36	chr3:49002200-49023800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:49002200-49023800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr3:49002200-49024400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr3:49002200-49024400	Strong transcription	Adipose Nuclei	Adipose
40	chr3:49002200-49024400	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr3:49002200-49024400	Strong transcription	Thymus	Thymus
42	chr3:49002200-49024600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:49002400-49012800	Strong transcription	Right Ventricle	heart
44	chr3:49002400-49020200	Strong transcription	Left Ventricle	heart
45	chr3:49002400-49023200	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr3:49002400-49024600	Strong transcription	Fetal Muscle Leg	muscle
47	chr3:49002400-49024600	Strong transcription	Stomach Smooth Muscle	stomach
48	chr3:49002400-49026600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr3:49002400-49026600	Weak transcription	Right Atrium	heart
50	chr3:49002800-49015000	Strong transcription	Placenta	Placenta

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