Variant report

Variant	rs34065644
Chromosome Location	chr11:62371938-62371939
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:62371911-62372328	HepG2	liver:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:62370041..62371967-chr11:62445972..62447850,2	K562	blood:
2	chr11:62371312..62376313-chr11:62493293..62497173,4	MCF-7	breast:
3	chr11:62370304..62373223-chr11:62654610..62657267,2	K562	blood:
4	chr11:62367185..62372634-chr11:62607154..62610784,6	MCF-7	breast:
5	chr11:62370075..62372268-chr11:62419892..62421743,2	MCF-7	breast:
6	chr11:62361223..62372590-chr11:62430599..62435389,30	K562	blood:
7	chr11:62355264..62375429-chr11:62428418..62443271,77	MCF-7	breast:
8	chr11:62371327..62373689-chr11:62412733..62415547,2	MCF-7	breast:
9	chr11:62365338..62373022-chr11:62621930..62625872,13	K562	blood:
10	chr11:62363464..62373052-chr11:62429645..62434985,23	K562	blood:
11	chr11:62370780..62373871-chr11:62607521..62610506,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000254964	TF binding region
MTA2	TF binding region
EML3	TF binding region
ENSG00000234857	Chromatin interaction
ENSG00000214753	Chromatin interaction
ENSG00000204922	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000162222	Chromatin interaction
ENSG00000162194	Chromatin interaction
ENSG00000255717	Chromatin interaction
ENSG00000162191	Chromatin interaction
ENSG00000168003	Chromatin interaction
ENSG00000255432	Chromatin interaction
ENSG00000089597	Chromatin interaction
ENSG00000206597	Chromatin interaction
ENSG00000185085	Chromatin interaction
ENSG00000214756	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1061093	0.80[ASN][1000 genomes]
rs11231137	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11231141	0.80[ASN][1000 genomes]
rs11231144	0.80[ASN][1000 genomes]
rs11231145	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11231150	0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11231151	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11231152	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs11231154	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11231155	0.88[ASN][1000 genomes]
rs11231156	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11231161	0.81[ASN][1000 genomes]
rs12049914	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12223627	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12225213	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12226821	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1801144	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2516633	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2516634	0.88[ASN][1000 genomes]
rs2849030	0.88[ASN][1000 genomes]
rs2849031	0.88[ASN][1000 genomes]
rs34894392	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs35587183	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35880596	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3923805	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60098285	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61296092	0.80[ASN][1000 genomes]
rs67308910	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7124057	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs71490390	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs71490392	0.80[AMR][1000 genomes]
rs71490394	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72927213	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72927237	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7928833	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7942154	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7942991	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7943191	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915636	chr11:62016992-62713565	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1441 gene(s)	inside rSNPs	diseases
2	nsv532283	chr11:62201358-62863475	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1433 gene(s)	inside rSNPs	diseases
3	nsv532284	chr11:62220043-62630253	Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1401 gene(s)	inside rSNPs	diseases
4	esv3584599	chr11:62262742-62398050	Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
5	nsv832182	chr11:62295575-62462848	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
6	nsv825939	chr11:62326083-62410577	Flanking Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
7	nsv497903	chr11:62330308-62608042	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	489 gene(s)	inside rSNPs	diseases
8	nsv555174	chr11:62334096-62496519	Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	243 gene(s)	inside rSNPs	diseases
9	nsv897622	chr11:62366986-62392229	Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs34065644	MTA2	cis	temporal cortex	BrainEAC
rs34065644	EEF1G	cis	multi-tissue	Pritchard
rs34065644	EML3	cis	Esophagus Mucosa	GTEx
rs34065644	MTA2	cis	brain	BrainEAC
rs34065644	EML3	cis	Whole Blood	GTEx
rs34065644	MTA2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:62369800-62372000	Weak transcription	HepG2	liver
2	chr11:62370000-62372000	Weak transcription	A549	lung
3	chr11:62370000-62375200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr11:62370000-62378800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr11:62370200-62372600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr11:62370200-62372600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr11:62370200-62375000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr11:62370200-62379000	Weak transcription	Fetal Kidney	kidney
9	chr11:62370400-62372600	Genic enhancers	K562	blood
10	chr11:62370600-62372400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr11:62370600-62372600	Genic enhancers	Fetal Muscle Leg	muscle
12	chr11:62370600-62373400	Weak transcription	HMEC	breast
13	chr11:62370600-62375800	Weak transcription	NHEK	skin
14	chr11:62370600-62377200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr11:62370600-62378000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr11:62370600-62378600	Weak transcription	Small Intestine	intestine
17	chr11:62370600-62378800	Weak transcription	HSMMtube	muscle
18	chr11:62370800-62372400	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr11:62370800-62372400	Weak transcription	Aorta	Aorta
20	chr11:62370800-62372600	Weak transcription	Brain Hippocampus Middle	brain
21	chr11:62370800-62372800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr11:62370800-62372800	Weak transcription	Pancreas	Pancrea
23	chr11:62370800-62373000	Weak transcription	Colonic Mucosa	Colon
24	chr11:62370800-62373800	Strong transcription	Muscle Satellite Cultured Cells	--
25	chr11:62370800-62373800	Strong transcription	NHLF	lung
26	chr11:62370800-62374400	Strong transcription	Spleen	Spleen
27	chr11:62370800-62374800	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr11:62370800-62375000	Strong transcription	Primary B cells from peripheral blood	blood
29	chr11:62370800-62375000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr11:62370800-62375000	Weak transcription	HSMM	muscle
31	chr11:62370800-62375200	Weak transcription	Brain Substantia Nigra	brain
32	chr11:62370800-62375200	Weak transcription	NH-A	brain
33	chr11:62370800-62375400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr11:62370800-62375600	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr11:62370800-62375800	Weak transcription	Brain Angular Gyrus	brain
36	chr11:62370800-62377800	Strong transcription	Primary T cells from cord blood	blood
37	chr11:62370800-62378000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr11:62370800-62378000	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr11:62370800-62378000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr11:62370800-62378400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr11:62370800-62378400	Weak transcription	Left Ventricle	heart
42	chr11:62370800-62378600	Weak transcription	Psoas Muscle	Psoas
43	chr11:62370800-62378600	Weak transcription	Right Atrium	heart
44	chr11:62371000-62372200	Weak transcription	Brain Anterior Caudate	brain
45	chr11:62371000-62372200	Strong transcription	Fetal Thymus	thymus
46	chr11:62371000-62372400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr11:62371000-62372600	Weak transcription	Duodenum Mucosa	Duodenum
48	chr11:62371000-62372600	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr11:62371000-62372600	Genic enhancers	Rectal Mucosa Donor 31	rectum
50	chr11:62371000-62373000	Weak transcription	Right Ventricle	heart

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