Variant report

Variant	rs9614129
Chromosome Location	chr22:30398078-30398079
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	chr22:30396260..30398091-chr22:30400736..30402849,2	K562	blood:
2	chr22:30392517..30394667-chr22:30396187..30399023,2	MCF-7	breast:

Extended variants
information (count: 65 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs12373962	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12484336	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12485243	0.84[AMR][1000 genomes]
rs16987156	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16988084	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs16988135	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28428766	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28522206	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28595572	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3788421	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57462999	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57653653	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs60665668	0.80[AMR][1000 genomes]
rs61352751	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7284538	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7285751	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7285885	0.80[AMR][1000 genomes]
rs7286551	0.84[AMR][1000 genomes]
rs7286905	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7290085	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7292732	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73161050	0.84[AMR][1000 genomes]
rs73161074	0.86[AMR][1000 genomes]
rs73161099	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73162731	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73162773	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73883345	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8138677	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8139217	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8140366	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8140770	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9306466	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9608822	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9608823	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9608836	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9608843	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9608845	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9608847	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs9614063	0.84[AMR][1000 genomes]
rs9614071	0.90[AMR][1000 genomes]
rs9614075	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9614083	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9614087	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9614089	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9614097	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9614101	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9614105	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9614108	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9614109	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9614110	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9614111	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9614122	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9614124	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9614127	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9614128	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9614131	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9614132	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9614143	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9614144	0.84[AMR][1000 genomes]
rs9614145	0.84[AMR][1000 genomes]
rs9680595	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9680809	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9983	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[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	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9614129	MTMR3	cis	Adipose Subcutaneous	GTEx
rs9614129	MTMR3	cis	Nerve Tibial	GTEx
rs9614129	MTMR3	cis	Thyroid	GTEx
rs9614129	MTMR3	cis	lung	GTEx
rs9614129	MTMR3	Cis_1M	lymphoblastoid	RTeQTL
rs9614129	MTMR3	cis	Artery Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30350600-30402600	Weak transcription	Aorta	Aorta
2	chr22:30363400-30427800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr22:30367000-30426600	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr22:30375200-30403200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr22:30377600-30402800	Weak transcription	Fetal Brain Male	brain
6	chr22:30378200-30398800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr22:30384200-30398400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr22:30384200-30403800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr22:30384400-30404000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr22:30385000-30404000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr22:30386200-30402600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr22:30388000-30398400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr22:30388600-30398200	Weak transcription	Spleen	Spleen
14	chr22:30388600-30400800	Weak transcription	Brain Cingulate Gyrus	brain
15	chr22:30389000-30398600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr22:30389200-30398400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr22:30389200-30402600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr22:30389200-30403000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr22:30389200-30404200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr22:30389200-30409200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr22:30389200-30411600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr22:30389200-30411800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr22:30389400-30398200	Weak transcription	Thymus	Thymus
24	chr22:30389800-30400600	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr22:30390200-30398800	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr22:30390200-30398800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr22:30390200-30403200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr22:30390200-30434200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr22:30390800-30398400	Weak transcription	Primary hematopoietic stem cells	blood
30	chr22:30390800-30403000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr22:30391200-30402800	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr22:30391200-30411400	Weak transcription	Small Intestine	intestine
33	chr22:30391400-30398200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr22:30391400-30398600	Weak transcription	Brain Angular Gyrus	brain
35	chr22:30391400-30398600	Weak transcription	Right Ventricle	heart
36	chr22:30391400-30398800	Weak transcription	Gastric	stomach
37	chr22:30391400-30399400	Weak transcription	Brain Substantia Nigra	brain
38	chr22:30391400-30400800	Weak transcription	HSMMtube	muscle
39	chr22:30391400-30402600	Weak transcription	Ovary	ovary
40	chr22:30391400-30403000	Weak transcription	Pancreas	Pancrea
41	chr22:30391400-30403200	Weak transcription	Psoas Muscle	Psoas
42	chr22:30391400-30403600	Weak transcription	Hela-S3	cervix
43	chr22:30391400-30409800	Weak transcription	Fetal Heart	heart
44	chr22:30391400-30411600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr22:30391400-30433000	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr22:30391600-30400200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr22:30391600-30400200	Weak transcription	NHLF	lung
48	chr22:30391600-30404000	Weak transcription	Stomach Mucosa	stomach
49	chr22:30391600-30409800	Weak transcription	K562	blood
50	chr22:30391600-30417800	Weak transcription	Right Atrium	heart

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