Variant report

Variant	rs2888286
Chromosome Location	chr12:58333869-58333870
allele	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	GATA1	chr12:58333778-58335949	PBDE	blood:	n/a	chr12:58334695-58334704
2	CUX1	chr12:58333856-58335137	K562	blood:	n/a	n/a
3	IRF1	chr12:58333793-58335767	K562	blood:	n/a	chr12:58334452-58334462 chr12:58333824-58333838 chr12:58334448-58334462 chr12:58333828-58333842 chr12:58333829-58333840 chr12:58334450-58334464

No.	Distal block	Cell Line	Cell type
1	chr12:58160622..58162536-chr12:58333544..58335201,2	K562	blood:
2	chr12:58238851..58241260-chr12:58332365..58335429,3	K562	blood:
3	chr12:58239271..58242314-chr12:58333147..58337015,4	K562	blood:
4	chr12:58176490..58178791-chr12:58333525..58336024,3	K562	blood:
5	chr12:58297630..58299144-chr12:58332422..58334699,2	K562	blood:
6	chr12:58327474..58329106-chr12:58333139..58335115,2	MCF-7	breast:
7	chr12:58162992..58165092-chr12:58332637..58335110,2	MCF-7	breast:

Variant related genes	Relation type
XRCC6BP1	TF binding region
ENSG00000257698	TF binding region
ENSG00000037897	Chromatin interaction
ENSG00000175215	Chromatin interaction
ENSG00000111012	Chromatin interaction
ENSG00000123297	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs12816216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12822306	1.00[CHB][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12827346	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12829858	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12830273	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12831787	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17120038	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17120048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17120057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17120058	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17120198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17120201	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17120203	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2888287	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34080411	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34142683	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34170251	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs34221389	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34238095	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34300531	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs34437870	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34499234	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34567504	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35326083	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35364486	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35375157	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35712620	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35726562	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3829337	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56964775	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61015952	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61935800	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61935801	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6581160	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6581162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6581163	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7132343	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7133275	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7136078	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7137226	1.00[CHB][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7295307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7299512	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7303136	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7307628	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7962775	0.82[JPT][hapmap]
rs7968265	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7970948	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7971139	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7978519	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[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	nsv559046	chr12:58162085-58478598	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	261 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58330200-58334400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:58330200-58334400	Weak transcription	Colonic Mucosa	Colon
3	chr12:58330200-58334400	Weak transcription	Small Intestine	intestine
4	chr12:58330200-58334600	Weak transcription	Esophagus	oesophagus
5	chr12:58330200-58334600	Weak transcription	Left Ventricle	heart
6	chr12:58330200-58334600	Weak transcription	Lung	lung
7	chr12:58330200-58334600	Weak transcription	Pancreas	Pancrea
8	chr12:58330200-58334600	Weak transcription	Spleen	Spleen
9	chr12:58330200-58334800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr12:58330400-58334600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr12:58330400-58334600	Weak transcription	Placenta	Placenta
12	chr12:58330400-58334600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr12:58330600-58334000	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr12:58330600-58334000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr12:58330600-58334000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr12:58330600-58334200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr12:58330600-58334200	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr12:58330600-58334200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr12:58330600-58334200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr12:58330600-58334200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr12:58330600-58334200	Weak transcription	Brain Anterior Caudate	brain
22	chr12:58330600-58334200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr12:58330600-58334200	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr12:58330600-58334200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr12:58330600-58334400	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr12:58330600-58334400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr12:58330600-58334400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr12:58330600-58334400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr12:58330600-58334400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr12:58330600-58334400	Weak transcription	Adipose Nuclei	Adipose
31	chr12:58330600-58334400	Weak transcription	Brain Hippocampus Middle	brain
32	chr12:58330600-58334400	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr12:58330600-58334400	Weak transcription	Colon Smooth Muscle	Colon
34	chr12:58330600-58334400	Weak transcription	Duodenum Mucosa	Duodenum
35	chr12:58330600-58334400	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr12:58330600-58334400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr12:58330600-58334400	Weak transcription	Fetal Intestine Small	intestine
38	chr12:58330600-58334400	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr12:58330600-58334400	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr12:58330600-58334400	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr12:58330600-58334400	Weak transcription	Stomach Mucosa	stomach
42	chr12:58330600-58334400	Weak transcription	Stomach Smooth Muscle	stomach
43	chr12:58330600-58334400	Weak transcription	A549	lung
44	chr12:58330600-58334400	Weak transcription	HMEC	breast
45	chr12:58330600-58334400	Weak transcription	HSMMtube	muscle
46	chr12:58330600-58334400	Weak transcription	HUVEC	blood vessel
47	chr12:58330600-58334400	Weak transcription	NHDF-Ad	bronchial
48	chr12:58330600-58334400	Weak transcription	NHLF	lung
49	chr12:58330600-58334600	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr12:58330600-58334600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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