Variant report

Variant	rs6724078
Chromosome Location	chr2:11724159-11724160
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	EGR1	chr2:11724142-11724804	MCF-7	breast:	n/a	chr2:11724443-11724456 chr2:11724444-11724458 chr2:11724442-11724457
2	FOSL2	chr2:11724155-11724672	SK-N-SH	brain:	n/a	chr2:11724456-11724468 chr2:11724459-11724470 chr2:11724457-11724466 chr2:11724455-11724466 chr2:11724458-11724465 chr2:11724457-11724467 chr2:11724421-11724428 chr2:11724420-11724428 chr2:11724458-11724466
3	CTCF	chr2:11724020-11724170	SK-N-SH_RA	brain:	n/a	n/a
4	EGR1	chr2:11724102-11724834	HCT-116	colon:	n/a	chr2:11724443-11724456 chr2:11724444-11724458 chr2:11724442-11724457
5	NFIC	chr2:11724159-11724743	HepG2	liver:	n/a	n/a
6	E2F4	chr2:11724159-11724540	MCF10A-Er-Src	breast:	n/a	n/a
7	CTCF	chr2:11724080-11724230	HUVEC	blood vessel:	n/a	n/a
8	TCF12	chr2:11724111-11724831	SK-N-SH	brain:	n/a	n/a
9	RAD21	chr2:11724067-11724907	HCT-116	colon:	n/a	n/a
10	CTCF	chr2:11723903-11724964	SK-N-SH	brain:	n/a	chr2:11724557-11724575
11	MYBL2	chr2:11724089-11724787	HepG2	liver:	n/a	n/a
12	POLR2A	chr2:11712005-11732311	MCF-7	breast:	n/a	n/a
13	FOXA2	chr2:11722942-11724253	HepG2	liver:	n/a	chr2:11723592-11723604
14	CTCF	chr2:11724120-11724270	GM12864	blood:	n/a	n/a
15	JUN	chr2:11724035-11724879	K562	blood:	n/a	chr2:11724456-11724468 chr2:11724459-11724470 chr2:11724457-11724466 chr2:11724458-11724465 chr2:11724457-11724467 chr2:11724421-11724428 chr2:11724420-11724428 chr2:11724458-11724466
16	FOSL2	chr2:11724151-11724814	A549	lung:	n/a	chr2:11724456-11724468 chr2:11724459-11724470 chr2:11724457-11724466 chr2:11724455-11724466 chr2:11724458-11724465 chr2:11724457-11724467 chr2:11724421-11724428 chr2:11724420-11724428 chr2:11724458-11724466
17	FOSL2	chr2:11724159-11724750	MCF-7	breast:	n/a	chr2:11724456-11724468 chr2:11724459-11724470 chr2:11724457-11724466 chr2:11724455-11724466 chr2:11724458-11724465 chr2:11724457-11724467 chr2:11724421-11724428 chr2:11724420-11724428 chr2:11724458-11724466
18	MYBL2	chr2:11724142-11724739	HepG2	liver:	n/a	n/a
19	SIN3AK20	chr2:11721955-11724935	MCF-7	breast:	n/a	n/a
20	CTCF	chr2:11723948-11724979	HCT-116	colon:	n/a	chr2:11724557-11724575
21	RAD21	chr2:11724147-11724798	HepG2	liver:	n/a	n/a
22	EGR1	chr2:11724077-11724885	HCT-116	colon:	n/a	chr2:11724443-11724456 chr2:11724444-11724458 chr2:11724442-11724457
23	FOSL2	chr2:11724115-11724750	MCF-7	breast:	n/a	chr2:11724456-11724468 chr2:11724459-11724470 chr2:11724457-11724466 chr2:11724455-11724466 chr2:11724458-11724465 chr2:11724457-11724467 chr2:11724421-11724428 chr2:11724420-11724428 chr2:11724458-11724466
24	FOSL2	chr2:11723913-11725189	HepG2	liver:	n/a	chr2:11724456-11724468 chr2:11724459-11724470 chr2:11724457-11724466 chr2:11724455-11724466 chr2:11724458-11724465 chr2:11724457-11724467 chr2:11724421-11724428 chr2:11724420-11724428 chr2:11724458-11724466
25	JUND	chr2:11724045-11724876	SK-N-SH	brain:	n/a	chr2:11724456-11724467 chr2:11724456-11724468 chr2:11724459-11724470 chr2:11724457-11724466 chr2:11724458-11724465 chr2:11724457-11724467 chr2:11724421-11724428 chr2:11724420-11724428 chr2:11724458-11724466
26	FOXM1	chr2:11724130-11724788	GM12878	blood:	n/a	n/a
27	CTCF	chr2:11723992-11724968	A549	lung:	n/a	chr2:11724557-11724575
28	RAD21	chr2:11723990-11724995	SK-N-SH	brain:	n/a	n/a
29	TEAD4	chr2:11724070-11724803	HepG2	liver:	n/a	n/a
30	MBD4	chr2:11724090-11724799	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:11272046..11273363-chr2:11723821..11725006,6	K562	blood:
2	chr2:11723075..11724603-chr2:11731951..11734172,2	MCF-7	breast:
3	chr2:11723582..11725102-chr2:11727716..11730148,2	K562	blood:
4	chr2:11557796..11559144-chr2:11724145..11724865,3	K562	blood:

Variant related genes	Relation type
GREB1	TF binding region
RN7SL674P	TF binding region
ENSG00000145063	Chromatin interaction
ENSG00000196208	Chromatin interaction
ENSG00000150873	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs13004648	0.87[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs13009660	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34507933	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35023351	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35188552	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35217326	0.85[EUR][1000 genomes]
rs35587928	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs36030386	0.86[EUR][1000 genomes]
rs6736604	0.95[EUR][1000 genomes]
rs6743256	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7559835	0.94[CEU][hapmap];0.95[EUR][1000 genomes]
rs7576944	0.94[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs9287733	0.94[CEU][hapmap];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv873663	chr2:11664349-11783775	Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6724078	TP53TG5	trans	cerebellum	SCAN
rs6724078	GREB1	cis	parietal	SCAN

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11678400-11757000	Weak transcription	Right Ventricle	heart
2	chr2:11694800-11755200	Weak transcription	Gastric	stomach
3	chr2:11700000-11767000	Weak transcription	Right Atrium	heart
4	chr2:11709800-11724200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:11711600-11738600	Weak transcription	Left Ventricle	heart
6	chr2:11714400-11765000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr2:11717600-11767000	Weak transcription	Fetal Intestine Small	intestine
8	chr2:11719200-11725800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr2:11719200-11738000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr2:11719400-11750800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:11720000-11735600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:11721600-11733000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:11721800-11726000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:11722000-11724600	Enhancers	Fetal Muscle Leg	muscle
15	chr2:11722000-11725600	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr2:11722200-11724600	Enhancers	Fetal Muscle Trunk	muscle
17	chr2:11722400-11724400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr2:11722400-11724400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:11722600-11724200	Enhancers	Pancreas	Pancrea
20	chr2:11722600-11724400	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr2:11722600-11724800	Enhancers	Stomach Smooth Muscle	stomach
22	chr2:11722600-11724800	Enhancers	HSMMtube	muscle
23	chr2:11722800-11724200	Enhancers	Placenta	Placenta
24	chr2:11722800-11724200	Enhancers	Ovary	ovary
25	chr2:11722800-11724400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:11722800-11724400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr2:11722800-11724400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr2:11722800-11724400	Enhancers	Fetal Stomach	stomach
29	chr2:11722800-11724400	Enhancers	HSMM	muscle
30	chr2:11722800-11724800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:11722800-11724800	Enhancers	Stomach Mucosa	stomach
32	chr2:11722800-11724800	Enhancers	NHDF-Ad	bronchial
33	chr2:11723000-11724200	Enhancers	Colon Smooth Muscle	Colon
34	chr2:11723000-11724400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr2:11723000-11724400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr2:11723000-11724600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:11723000-11724600	Enhancers	Brain Anterior Caudate	brain
38	chr2:11723000-11724800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr2:11723000-11724800	Enhancers	NH-A	brain
40	chr2:11723000-11725400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr2:11723000-11740400	Weak transcription	Liver	Liver
42	chr2:11723200-11724200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr2:11723200-11724200	Enhancers	A549	lung
44	chr2:11723200-11724400	Enhancers	NHLF	lung
45	chr2:11723200-11724400	Enhancers	Osteobl	bone
46	chr2:11723200-11724800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr2:11723200-11724800	Enhancers	Muscle Satellite Cultured Cells	--
48	chr2:11723200-11724800	Enhancers	Cortex derived primary cultured neurospheres	brain
49	chr2:11723200-11724800	Enhancers	Brain Angular Gyrus	brain
50	chr2:11723200-11724800	Enhancers	Skeletal Muscle Male	skeletal muscle

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