Variant report

Variant	rs4974091
Chromosome Location	chr3:49025101-49025102
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMC3	chr3:49025081-49025670	SK-N-SH	brain:	n/a	chr3:49025438-49025452

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:49024968..49025867-chr3:49051237..49052091,2	K562	blood:
2	chr3:48720909..48723341-chr3:49022618..49025566,2	K562	blood:

Variant related genes	Relation type
ENSG00000273211	TF binding region
ENSG00000235236	TF binding region
P4HTM	TF binding region
ENSG00000213672	Chromatin interaction
ENSG00000178252	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10780033	0.87[EUR][1000 genomes]
rs11130176	0.84[EUR][1000 genomes]
rs1134591	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11705737	0.91[EUR][1000 genomes]
rs11920534	0.89[EUR][1000 genomes]
rs11924597	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12491743	0.84[EUR][1000 genomes]
rs12493289	0.87[EUR][1000 genomes]
rs12637037	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13064784	0.83[EUR][1000 genomes]
rs13064883	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13064911	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13072911	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13076394	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13078308	0.82[EUR][1000 genomes]
rs13315711	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13316620	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28642807	0.88[EUR][1000 genomes]
rs4072859	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4974079	0.87[EUR][1000 genomes]
rs4974080	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4974082	0.92[EUR][1000 genomes]
rs4974084	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4974085	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4974087	0.88[EUR][1000 genomes]
rs6414613	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6446196	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6446198	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6446205	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6446252	0.87[EUR][1000 genomes]
rs6446253	0.86[EUR][1000 genomes]
rs6768433	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6781790	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6786665	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6789285	0.92[EUR][1000 genomes]
rs6791234	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6795025	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7372149	0.86[EUR][1000 genomes]
rs7373778	0.83[EUR][1000 genomes]
rs7373790	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7430198	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7430501	0.87[EUR][1000 genomes]
rs7431710	0.89[EUR][1000 genomes]
rs7431857	0.87[EUR][1000 genomes]
rs7432989	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7612459	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7615235	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7615675	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7621015	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7623023	0.85[EUR][1000 genomes]
rs7626445	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7627404	0.84[EUR][1000 genomes]
rs7628719	0.92[EUR][1000 genomes]
rs7636057	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7639332	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7643368	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7647093	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7649458	0.85[EUR][1000 genomes]
rs8926	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9311430	0.84[EUR][1000 genomes]
rs9311432	0.84[EUR][1000 genomes]
rs9311433	0.84[EUR][1000 genomes]
rs9311434	0.85[EUR][1000 genomes]
rs9681717	0.87[EUR][1000 genomes]
rs9682444	0.84[EUR][1000 genomes]
rs9754878	0.87[EUR][1000 genomes]
rs9755490	0.87[EUR][1000 genomes]
rs9830636	0.82[EUR][1000 genomes]
rs9835307	0.84[EUR][1000 genomes]
rs9840050	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9840684	0.87[EUR][1000 genomes]
rs9846123	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9850134	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9867373	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9876848	0.84[EUR][1000 genomes]
rs9879971	0.87[EUR][1000 genomes]
rs9884022	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs4974091	NICN1	cis	Thyroid	GTEx
rs4974091	AMT	cis	Muscle Skeletal	GTEx
rs4974091	WDR6	cis	Whole Blood	GTEx
rs4974091	WDR6	cis	Esophagus Mucosa	GTEx
rs4974091	WDR6	cis	Stomach	GTEx
rs4974091	WDR6	cis	Adipose Subcutaneous	GTEx
rs4974091	CCDC36	cis	Artery Tibial	GTEx
rs4974091	WDR6	cis	Nerve Tibial	GTEx
rs4974091	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs4974091	AMT	cis	Thyroid	GTEx
rs4974091	WDR6	cis	Muscle Skeletal	GTEx
rs4974091	WDR6	cis	lung	GTEx
rs4974091	CCDC36	cis	Esophagus Muscularis	GTEx
rs4974091	NCKIPSD	cis	Nerve Tibial	GTEx
rs4974091	NCKIPSD	cis	Muscle Skeletal	GTEx
rs4974091	WDR6	cis	Esophagus Muscularis	GTEx
rs4974091	WDR6	cis	Artery Tibial	GTEx
rs4974091	NICN1-AS1	cis	Thyroid	GTEx
rs4974091	NCKIPSD	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49002400-49026600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:49002400-49026600	Weak transcription	Right Atrium	heart
3	chr3:49005400-49027000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:49008200-49026600	Weak transcription	Stomach Mucosa	stomach
5	chr3:49018800-49026400	Weak transcription	Small Intestine	intestine
6	chr3:49018800-49026600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:49019600-49025200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr3:49019800-49025800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr3:49020000-49026600	Weak transcription	Fetal Kidney	kidney
10	chr3:49020800-49026600	Weak transcription	Psoas Muscle	Psoas
11	chr3:49021400-49026400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr3:49021400-49026600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr3:49021600-49026000	Weak transcription	Fetal Brain Male	brain
14	chr3:49021600-49026600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:49022200-49025400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr3:49022200-49026600	Weak transcription	Colonic Mucosa	Colon
17	chr3:49022200-49026600	Weak transcription	Fetal Lung	lung
18	chr3:49022400-49026400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr3:49022600-49025200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr3:49022600-49025600	Weak transcription	Pancreas	Pancrea
21	chr3:49022600-49026400	Weak transcription	Primary B cells from cord blood	blood
22	chr3:49022600-49026600	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr3:49022600-49026600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:49022600-49026600	Weak transcription	NHDF-Ad	bronchial
25	chr3:49022800-49025200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr3:49022800-49025200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr3:49022800-49025200	Weak transcription	Brain Substantia Nigra	brain
28	chr3:49022800-49026200	Weak transcription	HepG2	liver
29	chr3:49022800-49026400	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr3:49022800-49026400	Weak transcription	Right Ventricle	heart
31	chr3:49022800-49026600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr3:49022800-49026600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr3:49022800-49026600	Weak transcription	Esophagus	oesophagus
34	chr3:49022800-49026600	Weak transcription	HMEC	breast
35	chr3:49023000-49026400	Weak transcription	Fetal Heart	heart
36	chr3:49023000-49026600	Weak transcription	A549	lung
37	chr3:49023000-49026600	Weak transcription	NHEK	skin
38	chr3:49023200-49025200	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr3:49023200-49025200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr3:49023200-49026400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr3:49023200-49026600	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr3:49023200-49026600	Weak transcription	Primary B cells from peripheral blood	blood
43	chr3:49023400-49025200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr3:49023400-49026400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr3:49023400-49026400	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr3:49023400-49026400	Weak transcription	NH-A	brain
47	chr3:49023400-49026600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr3:49023400-49026600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr3:49023400-49026600	Weak transcription	Colon Smooth Muscle	Colon
50	chr3:49023400-49026600	Weak transcription	NHLF	lung

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