Variant report

Variant	rs17012763
Chromosome Location	chr2:33516437-33516438
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	GATA2	chr2:33516374-33516890	HUVEC	blood vessel:	n/a	n/a
2	JUND	chr2:33516349-33516926	A549	lung:	n/a	n/a
3	EP300	chr2:33516376-33516781	HepG2	liver:	n/a	n/a
4	ATF3	chr2:33516228-33516950	A549	lung:	n/a	n/a
5	FOS	chr2:33516201-33516899	MCF10A-Er-Src	breast:	n/a	chr2:33516647-33516658
6	FOXA2	chr2:33516428-33516743	HepG2	liver:	n/a	n/a
7	EP300	chr2:33516342-33516629	SK-N-SH_RA	brain:	n/a	n/a
8	FOXA2	chr2:33516270-33517069	A549	lung:	n/a	n/a
9	FOXA1	chr2:33516348-33516722	T-47D	breast:	n/a	chr2:33516548-33516563
10	STAT3	chr2:33516367-33516914	MCF10A-Er-Src	breast:	n/a	n/a
11	FOXA1	chr2:33516315-33516890	HepG2	liver:	n/a	chr2:33516548-33516563
12	ZBTB33	chr2:33516329-33516831	A549	lung:	n/a	n/a
13	FOSL2	chr2:33516028-33517105	A549	lung:	n/a	n/a
14	CEBPB	chr2:33516274-33516922	A549	lung:	n/a	n/a
15	KAP1	chr2:33516414-33517058	HEK293	kidney:	n/a	n/a
16	FOSL2	chr2:33516373-33516958	A549	lung:	n/a	n/a
17	FOS	chr2:33516385-33516832	MCF10A-Er-Src	breast:	n/a	chr2:33516647-33516658
18	NR3C1	chr2:33516354-33516824	A549	lung:	n/a	n/a
19	USF1	chr2:33516257-33517278	A549	lung:	n/a	n/a
20	SP1	chr2:33516089-33517253	A549	lung:	n/a	n/a
21	ZNF217	chr2:33516404-33516752	MCF-7	breast:	n/a	n/a
22	EP300	chr2:33516163-33517059	A549	lung:	n/a	chr2:33517010-33517024
23	NFIC	chr2:33516133-33517040	SK-N-SH	brain:	n/a	n/a
24	MYC	chr2:33516287-33516815	MCF10A-Er-Src	breast:	n/a	n/a
25	MAX	chr2:33516302-33517256	A549	lung:	n/a	chr2:33517004-33517013 chr2:33517003-33517014 chr2:33517004-33517013
26	FOXA1	chr2:33516422-33516762	T-47D	breast:	n/a	chr2:33516548-33516563
27	REST	chr2:33516389-33516782	A549	lung:	n/a	n/a
28	GABPA	chr2:33516277-33516975	A549	lung:	n/a	n/a
29	STAT3	chr2:33516381-33516848	MCF10A-Er-Src	breast:	n/a	n/a
30	STAT3	chr2:33516433-33516769	Hela-S3	cervix:	n/a	n/a
31	NFIC	chr2:33516347-33516824	HepG2	liver:	n/a	n/a
32	TCF12	chr2:33515710-33517267	A549	lung:	n/a	n/a
33	GATA3	chr2:33516143-33517122	A549	lung:	n/a	chr2:33517012-33517022
34	POLR2A	chr2:33516300-33516851	U87	brain:	n/a	n/a
35	FOS	chr2:33516357-33516985	HUVEC	blood vessel:	n/a	chr2:33516647-33516658
36	SIN3AK20	chr2:33516305-33516996	MCF-7	breast:	n/a	n/a
37	NFIC	chr2:33516381-33516901	SK-N-SH	brain:	n/a	n/a
38	GATA3	chr2:33516232-33516940	A549	lung:	n/a	n/a
39	FOXA1	chr2:33516309-33516869	HepG2	liver:	n/a	chr2:33516548-33516563
40	ZBTB33	chr2:33516281-33516962	A549	lung:	n/a	n/a
41	USF1	chr2:33516362-33517194	A549	lung:	n/a	n/a
42	EP300	chr2:33516178-33516955	SK-N-SH	brain:	n/a	n/a
43	TCF7L2	chr2:33516195-33516615	HepG2	liver:	n/a	chr2:33516580-33516594
44	SP1	chr2:33516131-33517212	A549	lung:	n/a	n/a
45	EP300	chr2:33516374-33516818	T-47D	breast:	n/a	n/a
46	GATA3	chr2:33516028-33517006	SK-N-SH	brain:	n/a	n/a
47	FOXA1	chr2:33516433-33516744	ECC-1	luminal epithelium:	n/a	chr2:33516548-33516563
48	NFIC	chr2:33516375-33516736	HepG2	liver:	n/a	n/a
49	TAF1	chr2:33516344-33516930	PFSK-1	brain:	n/a	n/a
50	TCF7L2	chr2:33516389-33517050	PANC-1	pancreas:	n/a	chr2:33516580-33516594

Variant related genes	Relation type
LTBP1	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11674005	0.87[EUR][1000 genomes]
rs11682866	1.00[CEU][hapmap]
rs11685019	0.87[EUR][1000 genomes]
rs11689160	1.00[CEU][hapmap]
rs11689377	1.00[CEU][hapmap]
rs11694122	1.00[CEU][hapmap]
rs11694765	1.00[CEU][hapmap]
rs17012718	0.91[YRI][hapmap];0.90[AFR][1000 genomes]
rs17012773	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs17012805	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs17038524	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1812485	1.00[MEX][hapmap]
rs55873210	0.87[EUR][1000 genomes]
rs56136117	0.82[AFR][1000 genomes]
rs56203414	0.82[EUR][1000 genomes]
rs57189309	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59830763	0.94[AFR][1000 genomes]
rs59953160	0.94[AFR][1000 genomes]
rs60912737	0.91[AFR][1000 genomes]
rs61151459	0.97[AFR][1000 genomes]
rs6708335	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs6730165	0.84[ASW][hapmap];0.93[LWK][hapmap];0.93[MKK][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes]
rs73925006	0.97[AFR][1000 genomes]
rs73925010	0.94[AFR][1000 genomes]
rs73927064	0.90[AFR][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	nsv998167	chr2:33074313-33541100	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv535623	chr2:33074313-33541100	Genic enhancers Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1005435	chr2:33136117-33747159	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
4	nsv535624	chr2:33136117-33747159	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
5	nsv873791	chr2:33489975-33586776	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
6	nsv1011020	chr2:33508811-33527784	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:33472000-33516600	Weak transcription	Psoas Muscle	Psoas
2	chr2:33492200-33516600	Weak transcription	Brain Hippocampus Middle	brain
3	chr2:33492200-33516600	Weak transcription	Brain Substantia Nigra	brain
4	chr2:33492400-33547400	Weak transcription	Fetal Intestine Small	intestine
5	chr2:33501200-33528800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:33501400-33516600	Weak transcription	K562	blood
7	chr2:33501800-33517800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr2:33502400-33516600	Weak transcription	Pancreas	Pancrea
9	chr2:33502400-33516600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr2:33502400-33516800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:33502400-33516800	Weak transcription	Esophagus	oesophagus
12	chr2:33502600-33537000	Weak transcription	Fetal Intestine Large	intestine
13	chr2:33503600-33518200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr2:33505000-33526200	Weak transcription	Placenta	Placenta
15	chr2:33507000-33528600	Weak transcription	Fetal Muscle Trunk	muscle
16	chr2:33513600-33516600	Weak transcription	Left Ventricle	heart
17	chr2:33514800-33516600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:33515200-33516600	Enhancers	Fetal Lung	lung
19	chr2:33515200-33516600	Enhancers	HSMMtube	muscle
20	chr2:33515200-33517000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr2:33515200-33517000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr2:33515200-33517000	Enhancers	Fetal Stomach	stomach
23	chr2:33515200-33519200	Enhancers	Fetal Heart	heart
24	chr2:33515400-33516600	Enhancers	Colon Smooth Muscle	Colon
25	chr2:33515400-33517000	Enhancers	Fetal Muscle Leg	muscle
26	chr2:33515600-33516600	Enhancers	Liver	Liver
27	chr2:33515600-33516600	Enhancers	Rectal Mucosa Donor 31	rectum
28	chr2:33515600-33516600	Weak transcription	Small Intestine	intestine
29	chr2:33515800-33516600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:33515800-33516600	Weak transcription	Aorta	Aorta
31	chr2:33515800-33516600	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr2:33515800-33516600	Enhancers	Hela-S3	cervix
33	chr2:33515800-33516600	Enhancers	HSMM	muscle
34	chr2:33515800-33517000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr2:33515800-33517200	Enhancers	Fetal Brain Female	brain
36	chr2:33515800-33517800	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr2:33516000-33516600	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr2:33516000-33516600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr2:33516000-33516600	Enhancers	Fetal Brain Male	brain
40	chr2:33516000-33516600	Enhancers	HepG2	liver
41	chr2:33516000-33516800	Enhancers	Brain Angular Gyrus	brain
42	chr2:33516000-33517200	Flanking Active TSS	A549	lung
43	chr2:33516000-33517400	Flanking Active TSS	HUVEC	blood vessel
44	chr2:33516000-33517800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr2:33516200-33516600	Enhancers	Duodenum Mucosa	Duodenum
46	chr2:33516200-33516600	Enhancers	Fetal Kidney	kidney
47	chr2:33516200-33517200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr2:33516200-33517200	Flanking Active TSS	NH-A	brain
49	chr2:33516400-33516600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr2:33516400-33516600	Enhancers	Adipose Nuclei	Adipose

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