Variant report

Variant	rs11231154
Chromosome Location	chr11:62362293-62362294
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:62361547-62362304	K562	blood:	n/a	n/a
2	POLR2A	chr11:62362291-62362777	K562	blood:	n/a	n/a
3	POLR2A	chr11:62362290-62362996	GM12892	blood:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:62313497..62315057-chr11:62360531..62363175,2	MCF-7	breast:
2	chr11:62362245..62364741-chr11:62437553..62440349,2	K562	blood:
3	chr11:62337877..62349012-chr11:62352905..62362829,37	MCF-7	breast:
4	chr11:62356516..62363396-chr11:62492172..62497480,8	K562	blood:
5	chr11:62358650..62362308-chr11:62559226..62561722,3	MCF-7	breast:
6	chr11:62361223..62372590-chr11:62430599..62435389,30	K562	blood:
7	chr11:62359506..62362353-chr11:62619695..62624770,4	K562	blood:
8	chr11:62359743..62362742-chr11:62413942..62417266,4	MCF-7	breast:
9	chr11:62355264..62375429-chr11:62428418..62443271,77	MCF-7	breast:
10	chr11:62359035..62362581-chr11:62419336..62421874,4	K562	blood:
11	chr11:62356781..62364031-chr11:62570003..62574737,9	K562	blood:
12	chr11:62361652..62363267-chr11:62402960..62404564,2	K562	blood:
13	chr11:62352847..62362753-chr11:62430170..62436741,21	K562	blood:
14	chr11:62361917..62364015-chr11:62443596..62445833,2	MCF-7	breast:

No data

Variant related genes	Relation type
MIR3654	TF binding region
TUT1	TF binding region
ENSG00000168569	Chromatin interaction
ENSG00000149016	Chromatin interaction
ENSG00000234857	Chromatin interaction
ENSG00000162222	Chromatin interaction
ENSG00000162191	Chromatin interaction
ENSG00000162231	Chromatin interaction
ENSG00000206597	Chromatin interaction
ENSG00000214756	Chromatin interaction
ENSG00000089597	Chromatin interaction
ENSG00000214753	Chromatin interaction
ENSG00000255717	Chromatin interaction
ENSG00000168003	Chromatin interaction
ENSG00000255508	Chromatin interaction
ENSG00000162194	Chromatin interaction
ENSG00000254772	Chromatin interaction
ENSG00000255432	Chromatin interaction
ENSG00000185085	Chromatin interaction
ENSG00000124942	Chromatin interaction
ENSG00000204922	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1061093	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11231138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11231141	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11231144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11231145	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11231150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11231151	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11231152	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11231155	0.96[CEU][hapmap];0.88[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11231156	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11231161	0.96[CEU][hapmap];0.84[GIH][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11231176	1.00[JPT][hapmap]
rs11553576	0.96[CEU][hapmap];0.81[GIH][hapmap];0.92[MEX][hapmap];0.88[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12049914	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12223627	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12225213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12226821	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12808829	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17773169	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1801144	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2428548	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs2428549	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs2428551	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2509961	0.87[CEU][hapmap];1.00[CHB][hapmap];0.92[MEX][hapmap];0.81[TSI][hapmap]
rs2509982	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs2512562	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs2512563	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs2516633	0.88[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.88[ASN][1000 genomes]
rs2516634	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2849030	0.96[CEU][hapmap];0.88[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2849031	0.96[CEU][hapmap];0.88[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34065644	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34894392	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35156678	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs35587183	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.81[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs35880596	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3923805	0.93[ASN][1000 genomes]
rs58720921	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60098285	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs61296092	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs67308910	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7124057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs71490390	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs71490392	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71490394	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72927213	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72927237	0.86[ASN][1000 genomes]
rs7928833	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7930896	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7937146	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7942154	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7942991	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.85[TSI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7943191	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][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	nsv832180	chr11:62201605-62364828	Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	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
8	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
9	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

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs11231154	C11orf48	cis	cerebellum	SCAN
rs11231154	EML3	cis	Esophagus Mucosa	GTEx
rs11231154	SCYL1	cis	parietal	SCAN
rs11231154	TUT1	cis	parietal	SCAN
rs11231154	EEF1G	cis	multi-tissue	Pritchard
rs11231154	SLC22A25	cis	parietal	SCAN
rs11231154	EEF1G///LOC729998	N/A	lymphoblastoid	RTeQTL
rs11231154	EML3	cis	multi-tissue	Pritchard
rs11231154	ROM1	cis	Thyroid	GTEx
rs11231154	CFL1	cis	parietal	SCAN
rs11231154	EML3	cis	cerebellum	SCAN
rs11231154	MTA2	cis	Esophagus Mucosa	GTEx
rs11231154	EML3	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:62359800-62368200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:62360000-62364400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr11:62360200-62366200	Strong transcription	Osteobl	bone
4	chr11:62360200-62366400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr11:62360200-62367200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr11:62360200-62367200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr11:62360400-62365200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr11:62360400-62366000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr11:62360400-62366000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr11:62360400-62366200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr11:62360400-62366200	Genic enhancers	Primary T cells fromperipheralblood	blood
12	chr11:62360400-62366200	Strong transcription	NH-A	brain
13	chr11:62360400-62367400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr11:62360600-62362800	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr11:62360600-62366000	Strong transcription	Fetal Stomach	stomach
16	chr11:62360600-62366200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr11:62360600-62366200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr11:62360600-62366200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr11:62360600-62366200	Strong transcription	NHLF	lung
20	chr11:62360800-62366200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr11:62360800-62366200	Strong transcription	Muscle Satellite Cultured Cells	--
22	chr11:62360800-62366200	Strong transcription	Colon Smooth Muscle	Colon
23	chr11:62360800-62366200	Strong transcription	HSMM	muscle
24	chr11:62360800-62366600	Strong transcription	Esophagus	oesophagus
25	chr11:62361000-62363000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr11:62361000-62366200	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr11:62361000-62366200	Strong transcription	Liver	Liver
28	chr11:62361000-62366200	Strong transcription	Fetal Intestine Small	intestine
29	chr11:62361000-62366200	Strong transcription	Left Ventricle	heart
30	chr11:62361000-62366400	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr11:62361000-62366600	Strong transcription	Fetal Intestine Large	intestine
32	chr11:62361000-62366800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr11:62361200-62362600	Weak transcription	Fetal Kidney	kidney
34	chr11:62361200-62365000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr11:62361200-62365800	Strong transcription	Aorta	Aorta
36	chr11:62361200-62365800	Strong transcription	Ovary	ovary
37	chr11:62361200-62365800	Strong transcription	Placenta Amnion	Placenta Amnion
38	chr11:62361200-62366000	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr11:62361200-62366000	Strong transcription	H9 Cell Line	embryonic stem cell
40	chr11:62361200-62366000	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr11:62361200-62366000	Strong transcription	Fetal Lung	lung
42	chr11:62361200-62366000	Strong transcription	HepG2	liver
43	chr11:62361200-62366200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
44	chr11:62361200-62366200	Strong transcription	Rectal Smooth Muscle	rectum
45	chr11:62361200-62366200	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr11:62361200-62366400	Strong transcription	HUES6 Cell Line	embryonic stem cell
47	chr11:62361200-62366400	Strong transcription	HSMMtube	muscle
48	chr11:62361200-62366600	Strong transcription	Colonic Mucosa	Colon
49	chr11:62361200-62366600	Strong transcription	Lung	lung
50	chr11:62361400-62362400	Weak transcription	Small Intestine	intestine

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