Variant report

Variant	rs1559989
Chromosome Location	chr2:231377995-231377996
allele	A/C/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	EP300	chr2:231377823-231378289	HepG2	liver:	n/a	chr2:231378234-231378248
2	FOXA2	chr2:231377710-231378551	HepG2	liver:	n/a	n/a
3	NR2F2	chr2:231377797-231378285	MCF-7	breast:	n/a	n/a
4	GATA3	chr2:231377752-231378507	A549	lung:	n/a	n/a
5	FOS	chr2:231377976-231378276	HUVEC	blood vessel:	n/a	chr2:231378128-231378139
6	TEAD4	chr2:231377806-231378330	HepG2	liver:	n/a	n/a
7	FOSL2	chr2:231377940-231378239	A549	lung:	n/a	n/a
8	EP300	chr2:231377837-231378323	HepG2	liver:	n/a	chr2:231378234-231378248
9	SP1	chr2:231377855-231378317	HepG2	liver:	n/a	n/a
10	HDAC2	chr2:231377781-231378455	HepG2	liver:	n/a	chr2:231378237-231378251 chr2:231378231-231378245 chr2:231378233-231378247 chr2:231378232-231378246 chr2:231378235-231378249 chr2:231378234-231378248
11	FOXA2	chr2:231377954-231378319	A549	lung:	n/a	n/a
12	HDAC2	chr2:231377926-231378288	MCF-7	breast:	n/a	chr2:231378237-231378251 chr2:231378231-231378245 chr2:231378233-231378247 chr2:231378232-231378246 chr2:231378235-231378249 chr2:231378234-231378248
13	NFIC	chr2:231377811-231378373	HepG2	liver:	n/a	n/a
14	FOXA2	chr2:231377611-231378340	HepG2	liver:	n/a	n/a
15	CEBPB	chr2:231377782-231378262	HepG2	liver:	n/a	n/a
16	FOXA1	chr2:231377609-231378472	HepG2	liver:	n/a	n/a
17	GATA2	chr2:231377830-231378480	HUVEC	blood vessel:	n/a	n/a
18	FOSL2	chr2:231377842-231378282	MCF-7	breast:	n/a	n/a
19	SP1	chr2:231377849-231378203	A549	lung:	n/a	n/a
20	HDAC2	chr2:231377804-231378468	HepG2	liver:	n/a	chr2:231378237-231378251 chr2:231378231-231378245 chr2:231378233-231378247 chr2:231378232-231378246 chr2:231378235-231378249 chr2:231378234-231378248
21	NR2F2	chr2:231377818-231378501	MCF-7	breast:	n/a	n/a
22	NR2F2	chr2:231377913-231378206	K562	blood:	n/a	n/a
23	FOXA1	chr2:231377839-231378424	HepG2	liver:	n/a	n/a
24	ELF1	chr2:231377585-231378084	HepG2	liver:	n/a	n/a
25	RFX5	chr2:231377845-231378039	Hela-S3	cervix:	n/a	n/a
26	ARID3A	chr2:231377869-231378453	HepG2	liver:	n/a	chr2:231378224-231378240
27	FOXA1	chr2:231377597-231378407	HepG2	liver:	n/a	n/a
28	CEBPB	chr2:231377867-231378195	A549	lung:	n/a	n/a
29	TCF12	chr2:231377768-231378380	A549	lung:	n/a	n/a
30	RCOR1	chr2:231377919-231378239	K562	blood:	n/a	n/a
31	SP1	chr2:231377803-231378308	A549	lung:	n/a	n/a
32	FOSL2	chr2:231377799-231378362	A549	lung:	n/a	n/a
33	FOXA1	chr2:231377807-231378449	HepG2	liver:	n/a	n/a
34	MAFK	chr2:231377925-231378240	HepG2	liver:	n/a	n/a
35	CEBPB	chr2:231377976-231378432	Hela-S3	cervix:	n/a	n/a
36	GATA3	chr2:231377851-231378552	MCF-7	breast:	n/a	n/a
37	JUND	chr2:231377927-231378229	HepG2	liver:	n/a	n/a
38	GATA3	chr2:231377793-231378477	MCF-7	breast:	n/a	n/a
39	MAFF	chr2:231377992-231378496	HepG2	liver:	n/a	n/a
40	POLR2A	chr2:231377828-231378370	HUVEC	blood vessel:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SP110-8	chr2:231377793-231378009	NONHSAT077293

Variant related genes	Relation type
HMGB1P3	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12991608	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12991681	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12992343	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13009809	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13031070	1.00[ASN][1000 genomes]
rs13035698	1.00[ASN][1000 genomes]
rs16827319	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17275036	1.00[ASN][1000 genomes]
rs28829019	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34078648	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35092618	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35485737	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35717626	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36078281	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36144939	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55759935	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60106579	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6705605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6728423	1.00[ASN][1000 genomes]
rs6729378	1.00[ASN][1000 genomes]
rs6742738	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6751402	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71355945	1.00[ASN][1000 genomes]
rs7576889	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7586695	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[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	esv18000	chr2:231072978-231467847	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:231355200-231380400	Strong transcription	Adipose Nuclei	Adipose
2	chr2:231355600-231378600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr2:231355800-231381400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr2:231359600-231380400	Weak transcription	Brain Hippocampus Middle	brain
5	chr2:231361800-231381400	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr2:231362200-231378600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr2:231362400-231378400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr2:231362400-231378600	Strong transcription	Primary T cells from cord blood	blood
9	chr2:231362600-231378600	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr2:231362600-231380600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr2:231363800-231380200	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr2:231364200-231381000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr2:231364600-231385800	Weak transcription	HSMMtube	muscle
14	chr2:231366600-231385200	Weak transcription	HMEC	breast
15	chr2:231366800-231379800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr2:231367000-231378600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr2:231368400-231378000	Strong transcription	Spleen	Spleen
18	chr2:231370800-231389600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr2:231371000-231409800	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr2:231371200-231384600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr2:231372000-231384600	Weak transcription	Placenta	Placenta
22	chr2:231372400-231379200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr2:231372400-231386200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr2:231372600-231378200	Weak transcription	Gastric	stomach
25	chr2:231372600-231379200	Weak transcription	NHLF	lung
26	chr2:231373600-231378000	Strong transcription	Left Ventricle	heart
27	chr2:231373800-231378000	Strong transcription	Aorta	Aorta
28	chr2:231374400-231378400	Strong transcription	Stomach Smooth Muscle	stomach
29	chr2:231374600-231378600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:231374800-231380200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr2:231375000-231378000	Weak transcription	Dnd41	blood
32	chr2:231375000-231378400	Weak transcription	Esophagus	oesophagus
33	chr2:231375000-231385600	Weak transcription	HSMM	muscle
34	chr2:231375200-231378600	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr2:231375200-231390200	Weak transcription	Ovary	ovary
36	chr2:231376200-231383400	Weak transcription	GM12878-XiMat	blood
37	chr2:231376400-231378200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr2:231376400-231378600	Weak transcription	Fetal Stomach	stomach
39	chr2:231376400-231379600	Weak transcription	Thymus	Thymus
40	chr2:231376400-231380200	Weak transcription	Fetal Thymus	thymus
41	chr2:231376400-231381200	Strong transcription	Primary B cells from cord blood	blood
42	chr2:231376400-231381800	Weak transcription	NHEK	skin
43	chr2:231376600-231378000	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr2:231376600-231378400	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr2:231376600-231380000	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr2:231376600-231381200	Strong transcription	Primary B cells from peripheral blood	blood
47	chr2:231376600-231381200	Weak transcription	NHDF-Ad	bronchial
48	chr2:231376600-231383600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr2:231376600-231384000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr2:231376600-231384400	Weak transcription	Primary hematopoietic stem cells	blood

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