Variant report

Variant	rs17046510
Chromosome Location	chr2:55180438-55180439
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	GATA3	chr2:55180272-55180743	MCF-7	breast:	n/a	n/a
2	FOXA1	chr2:55180329-55180745	T-47D	breast:	n/a	n/a
3	FOSL2	chr2:55179987-55180733	MCF-7	breast:	n/a	chr2:55180251-55180261 chr2:55180251-55180261 chr2:55180251-55180261
4	FOS	chr2:55180096-55180575	MCF10A-Er-Src	breast:	n/a	chr2:55180251-55180261 chr2:55180251-55180261 chr2:55180250-55180261 chr2:55180251-55180261
5	RAD21	chr2:55180355-55180814	MCF-7	breast:	n/a	n/a
6	ELF1	chr2:55180054-55180753	MCF-7	breast:	n/a	chr2:55180646-55180657
7	MAX	chr2:55180138-55180759	MCF-7	breast:	n/a	chr2:55180367-55180375
8	EP300	chr2:55180333-55180807	MCF-7	breast:	n/a	n/a
9	EP300	chr2:55180361-55180717	T-47D	breast:	n/a	n/a
10	SIN3AK20	chr2:55180056-55180954	MCF-7	breast:	n/a	n/a
11	GATA3	chr2:55180056-55180799	T-47D	breast:	n/a	n/a
12	HDAC2	chr2:55180259-55180813	MCF-7	breast:	n/a	n/a
13	SRF	chr2:55180225-55180764	MCF-7	breast:	n/a	n/a
14	ZNF217	chr2:55180296-55180759	MCF-7	breast:	n/a	n/a
15	POLR2A	chr2:55179997-55180771	PANC-1	pancreas:	n/a	n/a
16	TCF12	chr2:55179976-55180848	A549	lung:	n/a	chr2:55180515-55180524
17	FOXA1	chr2:55180343-55180735	T-47D	breast:	n/a	n/a
18	FOS	chr2:55180040-55180508	HUVEC	blood vessel:	n/a	chr2:55180251-55180261 chr2:55180251-55180261 chr2:55180250-55180261 chr2:55180251-55180261
19	FOSL2	chr2:55179925-55180749	A549	lung:	n/a	chr2:55180251-55180261 chr2:55180251-55180261 chr2:55179974-55179984 chr2:55180251-55180261
20	GATA3	chr2:55180300-55180706	MCF-7	breast:	n/a	n/a
21	GATA2	chr2:55180095-55180667	HUVEC	blood vessel:	n/a	n/a
22	GATA3	chr2:55180337-55180745	T-47D	breast:	n/a	n/a
23	GATA3	chr2:55179950-55180891	A549	lung:	n/a	n/a
24	NR2F2	chr2:55180173-55180792	MCF-7	breast:	n/a	n/a
25	GATA3	chr2:55179979-55181013	MCF-7	breast:	n/a	n/a
26	JUND	chr2:55180256-55180811	T-47D	breast:	n/a	n/a
27	NR2F2	chr2:55180185-55180838	MCF-7	breast:	n/a	n/a
28	SP1	chr2:55180022-55180768	A549	lung:	n/a	n/a
29	GATA3	chr2:55180225-55180835	A549	lung:	n/a	n/a
30	SIN3AK20	chr2:55180205-55180987	MCF-7	breast:	n/a	n/a
31	ELF1	chr2:55180159-55180795	MCF-7	breast:	n/a	chr2:55180646-55180657
32	JUND	chr2:55180357-55180799	MCF-7	breast:	n/a	n/a
33	TCF7L2	chr2:55180403-55180673	MCF-7	breast:	n/a	n/a
34	HDAC2	chr2:55180178-55180842	MCF-7	breast:	n/a	n/a
35	TCF7L2	chr2:55179858-55180748	PANC-1	pancreas:	n/a	n/a
36	GATA3	chr2:55180025-55180879	MCF-7	breast:	n/a	n/a
37	FOXA2	chr2:55180327-55180639	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55174500..55176023-chr2:55178242..55180647,2	MCF-7	breast:

Variant related genes	Relation type
EML6	TF binding region
ENSG00000214595	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs15029	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17046509	0.82[ASW][hapmap];0.95[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1992615	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4254542	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs57207110	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6718315	1.00[EUR][1000 genomes]
rs6729675	1.00[EUR][1000 genomes]
rs6747990	1.00[EUR][1000 genomes]
rs72910826	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72910837	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72910854	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72917588	1.00[EUR][1000 genomes]
rs7559999	1.00[EUR][1000 genomes]
rs7571562	1.00[EUR][1000 genomes]
rs7576504	1.00[EUR][1000 genomes]
rs7584654	1.00[EUR][1000 genomes]
rs7585495	1.00[EUR][1000 genomes]
rs7607946	1.00[EUR][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	nsv834069	chr2:55096597-55251680	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv582029	chr2:55159043-55204498	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55168800-55193400	Weak transcription	Primary B cells from peripheral blood	blood
2	chr2:55170400-55190400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:55173000-55193400	Weak transcription	Aorta	Aorta
4	chr2:55173200-55187000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr2:55173200-55203400	Weak transcription	Gastric	stomach
6	chr2:55173400-55184600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:55173600-55181200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:55173600-55194000	Weak transcription	Stomach Smooth Muscle	stomach
9	chr2:55173600-55195000	Weak transcription	Pancreas	Pancrea
10	chr2:55174800-55194000	Weak transcription	Brain Germinal Matrix	brain
11	chr2:55175400-55193200	Weak transcription	Fetal Brain Female	brain
12	chr2:55175600-55185600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr2:55175600-55185800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr2:55175600-55185800	Weak transcription	Brain Substantia Nigra	brain
15	chr2:55175600-55194600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr2:55175800-55181600	Weak transcription	Brain Anterior Caudate	brain
17	chr2:55175800-55184600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr2:55175800-55193800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr2:55176000-55182400	Weak transcription	Fetal Muscle Leg	muscle
20	chr2:55176000-55182800	Weak transcription	Fetal Intestine Small	intestine
21	chr2:55176200-55180600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr2:55176400-55184600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr2:55176600-55180800	Weak transcription	Fetal Muscle Trunk	muscle
24	chr2:55177800-55193800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr2:55178200-55193400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr2:55178400-55183000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr2:55178600-55193400	Weak transcription	Spleen	Spleen
28	chr2:55178800-55180600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:55178800-55180800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr2:55178800-55180800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:55178800-55180800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr2:55178800-55180800	Enhancers	HSMM	muscle
33	chr2:55178800-55183000	Enhancers	NHDF-Ad	bronchial
34	chr2:55178800-55183800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr2:55179000-55180600	Enhancers	NHLF	lung
36	chr2:55179600-55180600	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr2:55179600-55180800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr2:55179600-55180800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr2:55179600-55180800	Enhancers	Hela-S3	cervix
40	chr2:55179800-55180600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
41	chr2:55179800-55180600	Enhancers	GM12878-XiMat	blood
42	chr2:55179800-55180800	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr2:55179800-55180800	Enhancers	HUVEC	blood vessel
44	chr2:55180000-55180600	Flanking Active TSS	A549	lung
45	chr2:55180000-55180600	Enhancers	Monocytes-CD14+_RO01746	blood
46	chr2:55180000-55180600	Enhancers	NH-A	brain
47	chr2:55180000-55180600	Flanking Active TSS	Osteobl	bone
48	chr2:55180000-55182400	Enhancers	K562	blood
49	chr2:55180200-55181200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr2:55180200-55182800	Weak transcription	Sigmoid Colon	Sigmoid Colon

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