Variant report

Variant	rs901750
Chromosome Location	chr11:47209472-47209473
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:23)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:23 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HEY1	chr11:47208032-47209653	HepG2	liver:	n/a	chr11:47208076-47208091 chr11:47208189-47208204
2	POLR2A	chr11:47206648-47209488	Hela-S3	cervix:	n/a	n/a
3	EP300	chr11:47209327-47210221	SK-N-SH_RA	brain:	n/a	n/a
4	GATA2	chr11:47208472-47210224	SH-SY5Y	brain:	n/a	n/a
5	EP300	chr11:47207858-47210318	SK-N-SH	brain:	n/a	chr11:47208078-47208094 chr11:47208901-47208917
6	RCOR1	chr11:47209379-47209648	K562	blood:	n/a	n/a
7	USF2	chr11:47209403-47209739	Hela-S3	cervix:	n/a	chr11:47209545-47209556
8	GATA3	chr11:47209458-47209663	SH-SY5Y	brain:	n/a	n/a
9	USF1	chr11:47209409-47209674	SK-N-SH_RA	brain:	n/a	n/a
10	EP300	chr11:47209326-47210279	SK-N-SH_RA	brain:	n/a	n/a
11	RUNX3	chr11:47209293-47209602	GM12878	blood:	n/a	n/a
12	CEBPB	chr11:47209333-47209584	Hela-S3	cervix:	n/a	n/a
13	EGR1	chr11:47209389-47209624	K562	blood:	n/a	n/a
14	MAZ	chr11:47209434-47209525	HepG2	liver:	n/a	n/a
15	POLR2A	chr11:47205622-47209522	HepG2	liver:	n/a	n/a
16	RUNX3	chr11:47209251-47209573	GM12878	blood:	n/a	n/a
17	RCOR1	chr11:47208083-47209487	IMR90	lung:	n/a	n/a
18	MAX	chr11:47209399-47209571	Hela-S3	cervix:	n/a	n/a
19	USF1	chr11:47209425-47209660	SK-N-SH_RA	brain:	n/a	n/a
20	EBF1	chr11:47208839-47209630	GM12878	blood:	n/a	chr11:47209050-47209059 chr11:47209048-47209059
21	POLR2A	chr11:47208979-47209674	H1-neurons	neurons:	n/a	n/a
22	RCOR1	chr11:47209259-47209639	K562	blood:	n/a	n/a
23	POLR2A	chr11:47206428-47209519	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:47207085..47210178-chr11:47288214..47292056,4	MCF-7	breast:
2	chr11:47209362..47211566-chr11:47254961..47257621,2	MCF-7	breast:
3	chr11:47208508..47211092-chr11:47245771..47247789,2	MCF-7	breast:
4	chr11:47202119..47205492-chr11:47206060..47209673,5	K562	blood:
5	chr11:47205635..47209843-chr11:47268961..47271979,7	MCF-7	breast:
6	chr11:47205217..47215436-chr11:47233934..47241095,26	MCF-7	breast:
7	chr11:47204023..47207155-chr11:47207314..47211225,4	K562	blood:
8	chr11:47205689..47216568-chr11:47232414..47239487,27	MCF-7	breast:
9	chr11:47205110..47208888-chr11:47209275..47211677,6	MCF-7	breast:
10	chr11:47208035..47210761-chr11:47215071..47216625,2	K562	blood:
11	chr11:47209261..47211056-chr11:47214428..47216571,3	K562	blood:
12	chr11:47206281..47210029-chr11:47290997..47292963,3	K562	blood:
13	chr11:47205341..47210329-chr11:47212095..47213798,5	MCF-7	breast:
14	chr11:47208178..47210711-chr11:47292129..47294410,2	K562	blood:
15	chr11:47205837..47210171-chr11:47289770..47293955,7	MCF-7	breast:

No data

Variant related genes	Relation type
PACSIN3	TF binding region
ENSG00000134574	Chromatin interaction
ENSG00000256746	Chromatin interaction
ENSG00000243802	Chromatin interaction
ENSG00000025434	Chromatin interaction
ENSG00000134575	Chromatin interaction
ENSG00000165912	Chromatin interaction
ENSG00000110514	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11039122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11039131	0.82[ASN][1000 genomes]
rs12365578	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12803718	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1685404	0.84[CHB][hapmap];0.83[CHD][hapmap]
rs17787966	0.88[CEU][hapmap];0.94[CHB][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap]
rs2291443	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.84[YRI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2291444	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.84[YRI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3740690	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs752848	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs752850	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv897324	chr11:47193566-47212032	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs901750	C1QTNF4	cis	multi-tissue	Pritchard
rs901750	NUP160	cis	cerebellum	SCAN
rs901750	CTD-2384B9.1	cis	Nerve Tibial	GTEx
rs901750	C1QTNF4	cis	lymphoblastoid	seeQTL
rs901750	CKAP5	cis	parietal	SCAN
rs901750	PACSIN3	cis	parietal	SCAN
rs901750	MADD	cis	parietal	SCAN
rs901750	LRP4	cis	Nerve Tibial	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47206000-47210000	Flanking Active TSS	Stomach Smooth Muscle	stomach
2	chr11:47206400-47209600	Active TSS	H9 Cell Line	embryonic stem cell
3	chr11:47206600-47209600	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr11:47207400-47209600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
5	chr11:47208200-47209600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr11:47208200-47209600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr11:47208200-47209600	Bivalent Enhancer	Fetal Brain Male	brain
8	chr11:47208200-47209600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
9	chr11:47208200-47209600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
10	chr11:47208200-47209800	Flanking Active TSS	Hela-S3	cervix
11	chr11:47208200-47210200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
12	chr11:47208400-47209600	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
13	chr11:47208600-47209600	Active TSS	Right Ventricle	heart
14	chr11:47208600-47209800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr11:47208600-47211600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr11:47208800-47209600	Active TSS	Brain Anterior Caudate	brain
17	chr11:47208800-47210400	Enhancers	Fetal Lung	lung
18	chr11:47209000-47211600	Enhancers	Liver	Liver
19	chr11:47209200-47209600	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr11:47209200-47209600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
21	chr11:47209200-47209600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
22	chr11:47209200-47209600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr11:47209200-47209600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
24	chr11:47209200-47209600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr11:47209200-47209600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
26	chr11:47209200-47209600	Flanking Active TSS	Fetal Heart	heart
27	chr11:47209200-47209600	Bivalent Enhancer	Fetal Stomach	stomach
28	chr11:47209200-47209600	Enhancers	Pancreas	Pancrea
29	chr11:47209200-47209600	Flanking Active TSS	NHEK	skin
30	chr11:47209200-47209800	Enhancers	GM12878-XiMat	blood
31	chr11:47209200-47209800	Flanking Active TSS	Osteobl	bone
32	chr11:47209200-47210000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr11:47209200-47210000	Flanking Active TSS	HepG2	liver
34	chr11:47209200-47210200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr11:47209200-47210200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
36	chr11:47209200-47210200	Enhancers	A549	lung
37	chr11:47209200-47211400	Enhancers	Placenta Amnion	Placenta Amnion
38	chr11:47209200-47211400	Enhancers	NHDF-Ad	bronchial
39	chr11:47209200-47211800	Enhancers	Placenta	Placenta
40	chr11:47209200-47216000	Weak transcription	Esophagus	oesophagus
41	chr11:47209400-47209600	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
42	chr11:47209400-47209600	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
43	chr11:47209400-47209600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr11:47209400-47209600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
45	chr11:47209400-47209600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
46	chr11:47209400-47209600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
47	chr11:47209400-47209600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr11:47209400-47209600	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr11:47209400-47209600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr11:47209400-47209600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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