Variant report

Variant	rs4078937
Chromosome Location	chr11:70963861-70963862
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	SP1	chr11:70963735-70965234	A549	lung:	n/a	chr11:70964191-70964201 chr11:70963868-70963877 chr11:70964320-70964329 chr11:70963869-70963878 chr11:70964190-70964202 chr11:70963868-70963877 chr11:70964317-70964324 chr11:70963869-70963882 chr11:70963867-70963879 chr11:70964187-70964201 chr11:70964318-70964330 chr11:70963867-70963879 chr11:70964191-70964200 chr11:70964190-70964202 chr11:70964318-70964330
2	HDAC2	chr11:70963504-70965103	HepG2	liver:	n/a	chr11:70964766-70964780
3	TAF1	chr11:70963289-70963993	HepG2	liver:	n/a	n/a
4	POLR2A	chr11:70963723-70964780	HepG2	liver:	n/a	n/a
5	POLR2A	chr11:70962785-70963978	A549	lung:	n/a	n/a
6	CHD2	chr11:70963062-70963936	HepG2	liver:	n/a	n/a
7	FOXA1	chr11:70963811-70964883	HepG2	liver:	n/a	n/a
8	EP300	chr11:70963547-70965040	HepG2	liver:	n/a	n/a
9	SIN3A	chr11:70962349-70964475	H1-hESC	embryonic stem cell:	n/a	chr11:70962861-70962869 chr11:70963433-70963446 chr11:70963177-70963188
10	MAX	chr11:70962806-70964060	MCF-7	breast:	n/a	chr11:70963185-70963194 chr11:70963900-70963910 chr11:70963660-70963670
11	POLR2A	chr11:70962876-70964667	HepG2	liver:	n/a	n/a
12	NR2F2	chr11:70963505-70964071	MCF-7	breast:	n/a	n/a
13	SIN3AK20	chr11:70962876-70965150	MCF-7	breast:	n/a	n/a
14	MAX	chr11:70962880-70964765	A549	lung:	n/a	chr11:70963185-70963194 chr11:70963900-70963910 chr11:70963660-70963670
15	POLR2A	chr11:70962857-70964794	HepG2	liver:	n/a	n/a
16	MAZ	chr11:70962302-70965186	IMR90	lung:	n/a	chr11:70963185-70963194 chr11:70963900-70963910 chr11:70962364-70962373 chr11:70963660-70963670
17	POLR2A	chr11:70963190-70964019	MCF-7	breast:	n/a	n/a
18	TEAD4	chr11:70963779-70965039	HepG2	liver:	n/a	n/a
19	POLR2A	chr11:70962527-70964712	HepG2	liver:	n/a	n/a
20	HA-E2F1	chr11:70962411-70964671	MCF-7	breast:	n/a	chr11:70962870-70962880
21	MAX	chr11:70962604-70964897	HepG2	liver:	n/a	chr11:70963185-70963194 chr11:70963900-70963910 chr11:70963660-70963670
22	TBP	chr11:70963823-70964840	HepG2	liver:	n/a	n/a
23	MAX	chr11:70963748-70964086	HepG2	liver:	n/a	chr11:70963900-70963910
24	MAX	chr11:70962823-70964925	A549	lung:	n/a	chr11:70963185-70963194 chr11:70963900-70963910 chr11:70963660-70963670
25	POLR2A	chr11:70963340-70963943	H1-hESC	embryonic stem cell:	n/a	n/a
26	FOXA1	chr11:70963704-70964955	HepG2	liver:	n/a	n/a
27	POLR2A	chr11:70963255-70964257	MCF-7	breast:	n/a	n/a
28	POLR2A	chr11:70962868-70964080	MCF-7	breast:	n/a	n/a
29	POLR2A	chr11:70962887-70963997	H1-hESC	embryonic stem cell:	n/a	n/a
30	CREB1	chr11:70963317-70963997	A549	lung:	n/a	n/a
31	HEY1	chr11:70963252-70964695	HepG2	liver:	n/a	chr11:70963435-70963450 chr11:70963868-70963883 chr11:70964655-70964664
32	FOXA2	chr11:70963820-70964988	HepG2	liver:	n/a	n/a
33	BACH1	chr11:70963837-70963902	H1-hESC	embryonic stem cell:	n/a	n/a
34	HNF4G	chr11:70963739-70964801	HepG2	liver:	n/a	chr11:70964493-70964508 chr11:70964494-70964507 chr11:70964494-70964506 chr11:70964236-70964251 chr11:70964493-70964508
35	POLR2A	chr11:70963375-70963979	A549	lung:	n/a	n/a
36	BCL3	chr11:70963846-70964211	A549	lung:	n/a	n/a
37	FOXA1	chr11:70963846-70965055	HepG2	liver:	n/a	n/a
38	POLR2A	chr11:70963759-70964679	HepG2	liver:	n/a	n/a
39	MYC	chr11:70963586-70963908	MCF-7	breast:	n/a	chr11:70963660-70963670
40	EP300	chr11:70963434-70965236	HepG2	liver:	n/a	chr11:70965090-70965103
41	FOXA1	chr11:70963755-70964018	T-47D	breast:	n/a	n/a
42	SP1	chr11:70963805-70964970	A549	lung:	n/a	chr11:70964191-70964201 chr11:70963868-70963877 chr11:70964320-70964329 chr11:70963869-70963878 chr11:70964190-70964202 chr11:70963868-70963877 chr11:70964317-70964324 chr11:70963869-70963882 chr11:70963867-70963879 chr11:70964187-70964201 chr11:70964318-70964330 chr11:70963867-70963879 chr11:70964191-70964200 chr11:70964190-70964202 chr11:70964318-70964330
43	POLR2A	chr11:70963737-70963988	HepG2	liver:	n/a	n/a
44	POLR2A	chr11:70963319-70964002	A549	lung:	n/a	n/a
45	CEBPB	chr11:70963789-70964760	HepG2	liver:	n/a	chr11:70964714-70964727 chr11:70964018-70964031
46	CEBPD	chr11:70963494-70964422	HepG2	liver:	n/a	n/a
47	HNF4A	chr11:70963839-70964850	HepG2	liver:	n/a	chr11:70964493-70964508 chr11:70964492-70964507 chr11:70964494-70964507 chr11:70964494-70964506 chr11:70964493-70964508
48	HNF4A	chr11:70963805-70964789	HepG2	liver:	n/a	chr11:70964493-70964508 chr11:70964492-70964507 chr11:70964494-70964507 chr11:70964494-70964506 chr11:70964493-70964508
49	MAZ	chr11:70962886-70964750	HepG2	liver:	n/a	chr11:70963185-70963194 chr11:70963900-70963910 chr11:70963660-70963670
50	MYC	chr11:70963859-70963866	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:70963635..70965716-chr11:71014557..71017556,4	MCF-7	breast:
2	chr11:61519903..61520595-chr11:70963056..70964056,2	MCF-7	breast:
3	chr11:70856232..70858594-chr11:70962827..70965344,2	MCF-7	breast:
4	chr11:70950069..70955056-chr11:70960024..70964626,8	MCF-7	breast:
5	chr11:70962835..70965130-chr5:139026152..139027857,2	MCF-7	breast:

Variant related genes	Relation type
SHANK2	TF binding region
ENSG00000124920	Chromatin interaction
ENSG00000171604	Chromatin interaction
ENSG00000162105	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1004872	0.89[ASN][1000 genomes]
rs1372108	0.89[ASN][1000 genomes]
rs1985681	0.89[ASN][1000 genomes]
rs2919720	0.89[ASN][1000 genomes]
rs2919724	0.89[ASN][1000 genomes]
rs2919726	0.89[ASN][1000 genomes]
rs2919727	0.89[ASN][1000 genomes]
rs2919728	0.89[ASN][1000 genomes]
rs2919729	0.89[ASN][1000 genomes]
rs2919740	0.83[ASN][1000 genomes]
rs2919742	0.89[ASN][1000 genomes]
rs3020024	0.89[ASN][1000 genomes]
rs3020025	0.89[ASN][1000 genomes]
rs3020027	0.89[ASN][1000 genomes]
rs3020028	0.89[ASN][1000 genomes]
rs3020032	0.89[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048123	chr11:70795222-71231382	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:70961600-70964400	Bivalent Enhancer	Fetal Brain Male	brain
2	chr11:70961600-70964400	Active TSS	NHLF	lung
3	chr11:70961800-70964200	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
4	chr11:70961800-70964400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
5	chr11:70961800-70964400	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr11:70961800-70964400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr11:70962000-70964200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
8	chr11:70962000-70964200	Active TSS	Fetal Intestine Small	intestine
9	chr11:70962000-70964200	Active TSS	HSMM	muscle
10	chr11:70962000-70964400	Active TSS	H1 Cell Line	embryonic stem cell
11	chr11:70962000-70964400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr11:70962000-70964400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
13	chr11:70962000-70964600	Active TSS	H9 Cell Line	embryonic stem cell
14	chr11:70962000-70964800	Active TSS	A549	lung
15	chr11:70962200-70964000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
16	chr11:70962200-70964200	Active TSS	HSMMtube	muscle
17	chr11:70962200-70964400	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr11:70962200-70964400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
19	chr11:70962200-70964400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
20	chr11:70962200-70964400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr11:70962400-70964000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr11:70962400-70964000	Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr11:70962400-70964000	Bivalent/Poised TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr11:70962400-70964000	Bivalent/Poised TSS	Placenta	Placenta
25	chr11:70962400-70964000	Active TSS	Sigmoid Colon	Sigmoid Colon
26	chr11:70962400-70964200	Active TSS	Aorta	Aorta
27	chr11:70962400-70964200	Active TSS	Gastric	stomach
28	chr11:70962400-70964200	Active TSS	Placenta Amnion	Placenta Amnion
29	chr11:70962400-70964200	Bivalent/Poised TSS	Psoas Muscle	Psoas
30	chr11:70962400-70964200	Bivalent/Poised TSS	NHEK	skin
31	chr11:70962400-70964400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr11:70962400-70964400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr11:70962400-70964400	Active TSS	Duodenum Mucosa	Duodenum
34	chr11:70962400-70964400	Active TSS	Pancreas	Pancrea
35	chr11:70962600-70964200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr11:70962600-70964200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr11:70962600-70964200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr11:70962600-70964400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr11:70962800-70964000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr11:70963000-70964000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
41	chr11:70963000-70964400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
42	chr11:70963000-70964400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
43	chr11:70963000-70964400	Active TSS	Fetal Kidney	kidney
44	chr11:70963200-70964200	Enhancers	Spleen	Spleen
45	chr11:70963200-70964400	Active TSS	Esophagus	oesophagus
46	chr11:70963400-70964000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr11:70963400-70964000	Active TSS	Breast Myoepithelial Primary Cells	Breast
48	chr11:70963400-70964000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
49	chr11:70963400-70964000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
50	chr11:70963400-70964000	Active TSS	Brain Substantia Nigra	brain

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