Variant report

Variant	rs3018561
Chromosome Location	chr11:62392229-62392230
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10792355	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10792356	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10897289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231161	0.82[JPT][hapmap]
rs11231172	0.84[ASN][1000 genomes]
rs11231173	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11231176	0.86[CHB][hapmap]
rs11231181	0.86[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs11231182	0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11231183	0.92[ASN][1000 genomes]
rs12291465	0.92[ASN][1000 genomes]
rs12364753	0.82[ASN][1000 genomes]
rs12364756	0.82[ASN][1000 genomes]
rs13941	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[ASN][1000 genomes]
rs17637597	0.86[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs1893458	0.95[ASN][1000 genomes]
rs2956993	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2956995	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2957122	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2958236	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3017188	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3017666	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3809079	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4489748	0.86[CHB][hapmap];0.92[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs489778	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[ASN][1000 genomes]
rs597259	1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[ASN][1000 genomes]
rs60435036	0.84[ASN][1000 genomes]
rs644616	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.86[YRI][hapmap]
rs661182	0.95[ASN][1000 genomes]
rs67909703	0.90[ASN][1000 genomes]
rs693698	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.86[YRI][hapmap];0.92[ASN][1000 genomes]
rs7128852	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7949030	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9736354	0.82[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs3018561	CFL1	cis	parietal	SCAN
rs3018561	C11orf48	cis	cerebellum	SCAN
rs3018561	EML3	cis	Esophagus Mucosa	GTEx
rs3018561	EEF1G	cis	multi-tissue	Pritchard
rs3018561	GNG3	cis	cerebellum	SCAN
rs3018561	SLC22A25	cis	parietal	SCAN
rs3018561	TUT1	cis	parietal	SCAN
rs3018561	EML3	cis	cerebellum	SCAN
rs3018561	TTC9C	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:62389400-62392600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:62389400-62392800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr11:62389400-62393200	Weak transcription	Small Intestine	intestine
4	chr11:62389600-62392600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr11:62389600-62392600	Weak transcription	Primary T cells from cord blood	blood
6	chr11:62389600-62392600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr11:62389600-62392600	Weak transcription	Gastric	stomach
8	chr11:62389600-62392600	Weak transcription	Psoas Muscle	Psoas
9	chr11:62389600-62393200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr11:62389600-62393200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr11:62389600-62393600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr11:62389800-62392400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr11:62389800-62392600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr11:62389800-62392600	Weak transcription	Esophagus	oesophagus
15	chr11:62389800-62392600	Weak transcription	Ovary	ovary
16	chr11:62389800-62392600	Weak transcription	Spleen	Spleen
17	chr11:62390000-62392400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr11:62390000-62392400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr11:62390000-62392400	Weak transcription	Brain Germinal Matrix	brain
20	chr11:62390000-62392400	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr11:62390000-62392400	Weak transcription	Right Ventricle	heart
22	chr11:62390000-62392600	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr11:62390000-62392600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr11:62390000-62392600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr11:62390000-62392600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr11:62390000-62392600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr11:62390000-62392600	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr11:62390000-62392600	Weak transcription	Primary B cells from cord blood	blood
29	chr11:62390000-62392600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr11:62390000-62392600	Weak transcription	Aorta	Aorta
31	chr11:62390000-62392600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr11:62390000-62392600	Weak transcription	Brain Substantia Nigra	brain
33	chr11:62390000-62392600	Weak transcription	Duodenum Mucosa	Duodenum
34	chr11:62390000-62392600	Weak transcription	Fetal Intestine Large	intestine
35	chr11:62390000-62392600	Weak transcription	Fetal Lung	lung
36	chr11:62390000-62392600	Weak transcription	Left Ventricle	heart
37	chr11:62390000-62392600	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr11:62390000-62392600	Weak transcription	Rectal Smooth Muscle	rectum
39	chr11:62390000-62392600	Weak transcription	Dnd41	blood
40	chr11:62390000-62392600	Weak transcription	GM12878-XiMat	blood
41	chr11:62390000-62392800	Weak transcription	Fetal Kidney	kidney
42	chr11:62390000-62395400	Weak transcription	Fetal Brain Male	brain
43	chr11:62390000-62396200	Weak transcription	Fetal Heart	heart
44	chr11:62390000-62406800	Weak transcription	Right Atrium	heart
45	chr11:62390000-62413200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr11:62390200-62392400	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr11:62390200-62392400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr11:62390200-62392400	Weak transcription	Fetal Thymus	thymus
49	chr11:62390200-62392400	Weak transcription	A549	lung
50	chr11:62390200-62392400	Weak transcription	HSMMtube	muscle

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