Variant report

Variant	rs2956993
Chromosome Location	chr11:62406162-62406163
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:62406111-62406372	HepG2	liver:	n/a	n/a
2	POLR2A	chr11:62404410-62406406	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:62394749..62396582-chr11:62405094..62406897,2	K562	blood:
2	chr11:62400489..62403273-chr11:62403659..62406959,3	MCF-7	breast:
3	chr11:62387105..62391149-chr11:62405419..62408031,3	K562	blood:
4	chr11:62405002..62407043-chr11:62431738..62434084,2	MCF-7	breast:
5	chr11:62402497..62406808-chr11:62431018..62435715,5	MCF-7	breast:
6	chr11:62389393..62391048-chr11:62402932..62407168,5	MCF-7	breast:
7	chr11:62403450..62410109-chr11:62410421..62417583,11	K562	blood:
8	chr11:62404626..62407242-chr11:62418752..62422321,4	MCF-7	breast:

No data

Variant related genes	Relation type
GANAB	TF binding region
ENSG00000255432	Chromatin interaction
ENSG00000149541	Chromatin interaction
ENSG00000206597	Chromatin interaction
ENSG00000089597	Chromatin interaction
ENSG00000214756	Chromatin interaction
ENSG00000162194	Chromatin interaction
ENSG00000185085	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10792355	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10792356	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[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];0.95[ASN][1000 genomes]
rs11231161	0.82[JPT][hapmap]
rs11231172	0.90[ASN][1000 genomes]
rs11231173	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11231176	0.86[CHB][hapmap]
rs11231181	0.86[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs11231182	0.86[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11231183	0.97[ASN][1000 genomes]
rs12291465	0.97[ASN][1000 genomes]
rs12364753	0.87[ASN][1000 genomes]
rs12364756	0.87[ASN][1000 genomes]
rs13941	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.97[ASN][1000 genomes]
rs17637597	0.86[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs1893458	1.00[ASN][1000 genomes]
rs2956995	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2957122	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2958236	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3017188	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3017666	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3018561	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]
rs3809079	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4489748	0.86[CHB][hapmap];0.92[CHD][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs489778	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.97[ASN][1000 genomes]
rs597259	1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs60435036	0.90[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	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs67909703	0.95[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];0.97[ASN][1000 genomes]
rs7128852	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs71490397	0.82[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];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9736354	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
5	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
6	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
7	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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2956993	EML3	cis	Esophagus Mucosa	GTEx
rs2956993	TUT1	cis	parietal	SCAN
rs2956993	EML3	cis	cerebellum	SCAN
rs2956993	GNG3	cis	cerebellum	SCAN
rs2956993	CFL1	cis	parietal	SCAN
rs2956993	SLC22A25	cis	parietal	SCAN
rs2956993	TTC9C	cis	cerebellum	SCAN
rs2956993	EEF1G	cis	multi-tissue	Pritchard
rs2956993	C11orf48	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:62390000-62406800	Weak transcription	Right Atrium	heart
2	chr11:62390000-62413200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:62390400-62411800	Strong transcription	Fetal Intestine Small	intestine
4	chr11:62390600-62408600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr11:62390600-62412600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr11:62390800-62407400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr11:62390800-62407600	Strong transcription	Osteobl	bone
8	chr11:62390800-62412400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:62390800-62412400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr11:62391000-62407400	Strong transcription	Fetal Muscle Trunk	muscle
11	chr11:62391000-62408600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr11:62391000-62408800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr11:62391000-62412000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr11:62391200-62407400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr11:62391200-62407400	Strong transcription	Placenta	Placenta
16	chr11:62391200-62412400	Strong transcription	Fetal Stomach	stomach
17	chr11:62391400-62407000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr11:62392000-62407800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr11:62392000-62409200	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr11:62392000-62409200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr11:62392200-62406200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr11:62392200-62407000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr11:62392200-62407000	Strong transcription	Liver	Liver
24	chr11:62392200-62407400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr11:62392200-62407400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr11:62392200-62407400	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr11:62392400-62407000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr11:62392400-62407400	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr11:62392400-62407400	Strong transcription	Adipose Nuclei	Adipose
30	chr11:62392400-62407400	Strong transcription	Brain Germinal Matrix	brain
31	chr11:62392400-62407600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr11:62392400-62407600	Strong transcription	Fetal Thymus	thymus
33	chr11:62392400-62411800	Strong transcription	Fetal Muscle Leg	muscle
34	chr11:62392600-62406600	Strong transcription	Spleen	Spleen
35	chr11:62392600-62407000	Strong transcription	Thymus	Thymus
36	chr11:62392600-62407200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr11:62392600-62407200	Strong transcription	Rectal Mucosa Donor 31	rectum
38	chr11:62392600-62407200	Strong transcription	Skeletal Muscle Male	skeletal muscle
39	chr11:62392600-62407200	Strong transcription	GM12878-XiMat	blood
40	chr11:62392600-62407400	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr11:62392600-62407400	Strong transcription	H9 Cell Line	embryonic stem cell
42	chr11:62392600-62407400	Strong transcription	HUES48 Cell Line	embryonic stem cell
43	chr11:62392600-62407400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr11:62392600-62407400	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr11:62392600-62407400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr11:62392600-62407400	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr11:62392600-62407600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr11:62392600-62407600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr11:62392600-62407600	Strong transcription	Fetal Intestine Large	intestine
50	chr11:62392600-62407600	Strong transcription	Dnd41	blood

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