Variant report

Variant	rs1004769
Chromosome Location	chr2:167997817-167997818
allele	A/T
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	JUND	chr2:167997053-167997893	SK-N-SH	brain:	n/a	n/a
2	TEAD4	chr2:167997011-167997838	SK-N-SH	brain:	n/a	chr2:167997412-167997421
3	MAX	chr2:167997266-167997857	HCT-116	colon:	n/a	chr2:167997583-167997590 chr2:167997508-167997517
4	JUND	chr2:167996969-167998219	SK-N-SH	brain:	n/a	n/a
5	FOXM1	chr2:167997212-167997924	ECC-1	luminal epithelium:	n/a	n/a
6	RCOR1	chr2:167996872-167997829	IMR90	lung:	n/a	n/a
7	MAX	chr2:167997130-167997878	ECC-1	luminal epithelium:	n/a	chr2:167997583-167997590 chr2:167997508-167997517
8	NFIC	chr2:167997109-167997903	ECC-1	luminal epithelium:	n/a	n/a
9	MYC	chr2:167997141-167997883	MCF10A-Er-Src	breast:	n/a	chr2:167997583-167997590 chr2:167997508-167997517
10	GATA3	chr2:167996968-167997883	SK-N-SH	brain:	n/a	n/a
11	EP300	chr2:167996881-167997912	SK-N-SH	brain:	n/a	n/a
12	TCF12	chr2:167997063-167997831	ECC-1	luminal epithelium:	n/a	chr2:167997446-167997456
13	RXRA	chr2:167997116-167997842	SK-N-SH	brain:	n/a	chr2:167997323-167997332
14	MEF2A	chr2:167996971-167997877	SK-N-SH	brain:	n/a	chr2:167997592-167997607 chr2:167997700-167997716 chr2:167997265-167997286 chr2:167997700-167997717
15	EP300	chr2:167996970-167997858	SK-N-SH	brain:	n/a	n/a
16	MEF2A	chr2:167997020-167997901	SK-N-SH	brain:	n/a	chr2:167997592-167997607 chr2:167997700-167997716 chr2:167997265-167997286 chr2:167997700-167997717
17	PBX3	chr2:167997011-167997875	SK-N-SH	brain:	n/a	n/a
18	JUND	chr2:167997018-167997888	SK-N-SH	brain:	n/a	n/a
19	MYC	chr2:167997245-167997874	MCF10A-Er-Src	breast:	n/a	chr2:167997583-167997590 chr2:167997508-167997517
20	TCF12	chr2:167996965-167997919	SK-N-SH	brain:	n/a	chr2:167997446-167997456
21	NFIC	chr2:167997306-167997854	ECC-1	luminal epithelium:	n/a	n/a
22	POLR2A	chr2:167996990-167998155	PFSK-1	brain:	n/a	n/a
23	NFIC	chr2:167997051-167997949	SK-N-SH	brain:	n/a	n/a
24	GATA3	chr2:167996926-167997986	SK-N-SH	brain:	n/a	n/a
25	EP300	chr2:167996961-167997901	SK-N-SH	brain:	n/a	n/a
26	TCF12	chr2:167996882-167997931	SK-N-SH	brain:	n/a	chr2:167997446-167997456
27	EP300	chr2:167997050-167997895	ECC-1	luminal epithelium:	n/a	n/a
28	JUN	chr2:167997222-167997864	HUVEC	blood vessel:	n/a	n/a

Variant related genes	Relation type
XIRP2-AS1	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1004767	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs1004768	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs10497306	0.80[CEU][hapmap]
rs10497308	1.00[CEU][hapmap]
rs10497309	1.00[CEU][hapmap]
rs10497311	1.00[CEU][hapmap];0.86[YRI][hapmap]
rs10497312	1.00[CEU][hapmap]
rs10497313	1.00[CEU][hapmap]
rs10497318	1.00[CEU][hapmap]
rs10497320	1.00[CEU][hapmap]
rs1155283	1.00[CEU][hapmap];0.86[YRI][hapmap]
rs1429931	1.00[CEU][hapmap]
rs1429932	1.00[CEU][hapmap]
rs1479593	1.00[CEU][hapmap]
rs16853024	1.00[CEU][hapmap];0.86[YRI][hapmap]
rs16853028	0.82[EUR][1000 genomes]
rs16853035	0.82[EUR][1000 genomes]
rs16853052	1.00[CEU][hapmap]
rs16853103	1.00[CEU][hapmap]
rs16853180	1.00[CEU][hapmap]
rs16853181	1.00[CEU][hapmap]
rs16853201	1.00[CEU][hapmap]
rs17551389	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs17616012	0.80[CEU][hapmap]
rs17616439	0.80[EUR][1000 genomes]
rs17616712	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs2390515	1.00[CEU][hapmap]
rs2390548	1.00[CEU][hapmap]
rs6706115	1.00[CEU][hapmap]
rs6755389	1.00[CEU][hapmap];0.82[YRI][hapmap]
rs7556849	0.82[EUR][1000 genomes]
rs7565857	1.00[CEU][hapmap]
rs7578058	1.00[CEU][hapmap]
rs7586178	1.00[CEU][hapmap];0.86[YRI][hapmap]
rs7604418	1.00[CEU][hapmap]
rs7605024	1.00[CEU][hapmap]
rs989007	1.00[CEU][hapmap]
rs989008	1.00[CEU][hapmap]

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	nsv875376	chr2:167844513-168037489	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:167989200-167998600	Weak transcription	Left Ventricle	heart
2	chr2:167992200-167999800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr2:167993800-167999800	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr2:167995000-167999400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr2:167995000-167999600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr2:167996200-167998200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:167996200-167998400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:167996200-167998600	Enhancers	HMEC	breast
9	chr2:167996200-168001400	Enhancers	Fetal Heart	heart
10	chr2:167996200-168001400	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr2:167996600-167998200	Enhancers	HSMM	muscle
12	chr2:167996600-167998200	Enhancers	NHEK	skin
13	chr2:167996800-167998000	Enhancers	NH-A	brain
14	chr2:167996800-167998000	Enhancers	NHDF-Ad	bronchial
15	chr2:167996800-167998200	Enhancers	Muscle Satellite Cultured Cells	--
16	chr2:167996800-167998200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr2:167996800-167998200	Enhancers	Osteobl	bone
18	chr2:167997000-167998000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr2:167997000-167998200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr2:167997000-167999200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr2:167997200-167998600	Weak transcription	Stomach Smooth Muscle	stomach
22	chr2:167997200-167999400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr2:167997200-167999600	Weak transcription	Psoas Muscle	Psoas
24	chr2:167997400-167999600	Weak transcription	NHLF	lung
25	chr2:167997400-168001000	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr2:167997600-168000800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr2:167997800-167998400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:167997800-167998400	Weak transcription	Rectal Smooth Muscle	rectum

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