Variant report

Variant	rs11039426
Chromosome Location	chr11:47863119-47863120
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:47862976-47863194	MCF-7	breast:	n/a	n/a
2	POLR2A	chr11:47863020-47863139	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr11:47862931-47863995	GM12892	blood:	n/a	n/a
4	POLR2A	chr11:47862986-47863215	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr11:47862700-47863388	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr11:47862932-47863279	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr11:47863073-47863193	K562	blood:	n/a	n/a
8	POLR2A	chr11:47862861-47863304	K562	blood:	n/a	n/a
9	POLR2A	chr11:47862763-47863350	GM12892	blood:	n/a	n/a
10	POLR2A	chr11:47862746-47863315	K562	blood:	n/a	n/a
11	POLR2A	chr11:47862707-47863243	K562	blood:	n/a	n/a

Variant related genes	Relation type
NUP160	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10838747	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs10838748	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.81[ASN][1000 genomes]
rs10838757	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11039342	0.81[ASN][1000 genomes]
rs11039355	0.82[ASN][1000 genomes]
rs11039389	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11039390	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11039391	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11039416	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11039433	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11602339	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11602395	0.80[ASN][1000 genomes]
rs11605774	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12361031	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12361256	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12364432	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12418852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12421210	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12785833	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12787112	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]
rs12787330	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12798109	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12803191	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17788930	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2290850	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34128973	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34614231	0.84[AMR][1000 genomes]
rs34910028	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34923397	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35805829	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35902101	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35985502	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4752797	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4752801	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4752873	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7105282	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7120333	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7130758	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7927771	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7947730	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052397	chr11:47675470-48594256	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv832143	chr11:47700808-47883540	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv530620	chr11:47765455-48664555	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
4	nsv1036992	chr11:47794621-48666024	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv1049835	chr11:47837089-47928822	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv541036	chr11:47837089-47928822	Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:14)

SNP	Gene	Cis/trans	Tissue	Source
rs11039426	C1QTNF4	cis	Muscle Skeletal	GTEx
rs11039426	C1QTNF4	cis	Whole Blood	GTEx
rs11039426	MTCH2	cis	cerebellum	SCAN
rs11039426	C1QTNF4	cis	Esophagus Mucosa	GTEx
rs11039426	DGKZ	cis	cerebellum	SCAN
rs11039426	C1QTNF4	cis	lung	GTEx
rs11039426	C1QTNF4	cis	Skin Sun Exposed Lower leg	GTEx
rs11039426	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs11039426	SLC35C1	cis	parietal	SCAN
rs11039426	NDUFS3	Cis_1M	lymphoblastoid	RTeQTL
rs11039426	MADD	cis	cerebellum	SCAN
rs11039426	C1QTNF4	cis	Adipose Subcutaneous	GTEx
rs11039426	C1QTNF4	cis	lymphoblastoid	seeQTL
rs11039426	PSMC3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47790200-47869200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:47795400-47866600	Strong transcription	Fetal Thymus	thymus
3	chr11:47795400-47868400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:47796200-47867400	Strong transcription	Primary T cells fromperipheralblood	blood
5	chr11:47796200-47868200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr11:47796200-47868200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr11:47796200-47868400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr11:47796200-47868400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr11:47796200-47868600	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr11:47796400-47867600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr11:47796600-47868600	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr11:47798000-47868000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr11:47798400-47864800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr11:47807000-47865600	Strong transcription	Duodenum Mucosa	Duodenum
15	chr11:47820000-47864800	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr11:47831800-47868000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr11:47840600-47863600	Weak transcription	Stomach Mucosa	stomach
18	chr11:47846600-47864200	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr11:47846600-47867000	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr11:47847000-47868200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr11:47847200-47867400	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr11:47847600-47868000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr11:47847600-47868800	Strong transcription	Fetal Muscle Trunk	muscle
24	chr11:47847800-47865600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr11:47848200-47867200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr11:47849800-47865800	Strong transcription	Primary B cells from peripheral blood	blood
27	chr11:47850000-47867600	Strong transcription	Primary B cells from cord blood	blood
28	chr11:47850000-47868400	Strong transcription	Fetal Lung	lung
29	chr11:47850200-47864000	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr11:47850200-47867400	Strong transcription	Primary T cells from cord blood	blood
31	chr11:47850600-47868400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr11:47851200-47865200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr11:47851400-47868600	Strong transcription	Placenta	Placenta
34	chr11:47851600-47865800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr11:47851600-47866200	Strong transcription	Rectal Mucosa Donor 31	rectum
36	chr11:47851600-47867400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr11:47851800-47863600	Strong transcription	Dnd41	blood
38	chr11:47851800-47864600	Strong transcription	Stomach Smooth Muscle	stomach
39	chr11:47851800-47864800	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr11:47851800-47865200	Strong transcription	Adipose Nuclei	Adipose
41	chr11:47851800-47865400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr11:47851800-47867600	Strong transcription	Placenta Amnion	Placenta Amnion
43	chr11:47851800-47868000	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr11:47851800-47868000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr11:47852200-47864400	Strong transcription	Fetal Brain Female	brain
46	chr11:47852200-47865800	Strong transcription	Cortex derived primary cultured neurospheres	brain
47	chr11:47852200-47867600	Strong transcription	Thymus	Thymus
48	chr11:47852400-47864800	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr11:47852400-47865800	Strong transcription	Fetal Muscle Leg	muscle
50	chr11:47852400-47867200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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