Variant report

Variant	rs4233660
Chromosome Location	chr2:153578386-153578387
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	CEBPB	chr2:153578170-153578809	K562	blood:	n/a	n/a
2	GATA3	chr2:153578158-153578564	SH-SY5Y	brain:	n/a	n/a
3	CUX1	chr2:153578056-153578689	K562	blood:	n/a	n/a
4	GATA1	chr2:153578032-153578886	PBDE	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:153574994..153576922-chr2:153576951..153581012,5	MCF-7	breast:

Variant related genes	Relation type
PRPF40A	TF binding region
ENSG00000177917	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10172024	0.86[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs10181485	0.88[ASN][1000 genomes]
rs10200667	0.90[ASN][1000 genomes]
rs1036526	0.81[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs1065266	0.80[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs10931229	0.81[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs1128804	0.85[CHB][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs11544718	0.88[ASN][1000 genomes]
rs11899051	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12477881	0.86[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs12621561	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12997814	0.88[ASN][1000 genomes]
rs13005368	0.90[ASN][1000 genomes]
rs13010731	0.86[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs13017428	0.90[ASN][1000 genomes]
rs13031469	0.80[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs13419068	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1370498	0.80[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs1437678	0.81[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs16831548	0.80[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs16831740	0.85[CHB][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs17328734	0.85[CHB][hapmap];0.90[ASN][1000 genomes]
rs17400645	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs1962313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1986743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1992146	0.81[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs2118377	0.80[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs2304556	0.80[CHB][hapmap]
rs2304559	0.88[ASN][1000 genomes]
rs2346534	0.88[ASN][1000 genomes]
rs2346539	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2346540	0.98[ASN][1000 genomes]
rs2346541	0.90[ASN][1000 genomes]
rs2346542	0.86[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs2346543	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[ASN][1000 genomes]
rs2346549	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2346550	0.85[CHB][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs3171980	0.80[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs3175	0.81[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34585982	0.82[ASN][1000 genomes]
rs34668102	0.88[ASN][1000 genomes]
rs3748937	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3748938	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3748939	0.86[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs3762503	0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs3762506	0.88[ASN][1000 genomes]
rs3762507	0.80[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs3811566	0.90[ASN][1000 genomes]
rs3811567	0.82[CHB][hapmap]
rs4267470	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4580346	0.94[ASN][1000 genomes]
rs4664121	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4664122	0.81[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs4664601	0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs4664602	0.84[ASN][1000 genomes]
rs4664604	0.86[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs4664605	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4664606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4664607	0.86[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs4664609	0.99[ASN][1000 genomes]
rs4664610	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs56283545	0.83[ASN][1000 genomes]
rs61049574	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6434128	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs6434161	0.86[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs6434162	0.86[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs6713779	0.88[ASN][1000 genomes]
rs6723574	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6727279	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6744923	0.86[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs6746079	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6746321	0.88[ASN][1000 genomes]
rs6748160	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72871191	0.98[ASN][1000 genomes]
rs72872607	0.98[ASN][1000 genomes]
rs7556673	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7558920	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7559219	0.90[ASN][1000 genomes]
rs7560393	0.86[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs7570759	0.90[ASN][1000 genomes]
rs7576152	0.87[ASN][1000 genomes]
rs7576847	0.86[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs7582253	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7589899	0.81[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7592669	0.90[ASN][1000 genomes]
rs7593347	0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs7596408	0.80[CEU][hapmap];0.83[EUR][1000 genomes]
rs7599946	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7605709	0.90[ASN][1000 genomes]
rs7608603	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9288121	0.81[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs9288125	0.80[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs9288127	0.88[ASN][1000 genomes]
rs9646744	0.90[ASN][1000 genomes]
rs9789505	0.98[ASN][1000 genomes]
rs9789521	0.90[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834421	chr2:153470109-153664235	Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv3693438	chr2:153505376-153718246	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	esv1798142	chr2:153578113-153600123	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:153575800-153582800	Weak transcription	Lung	lung
2	chr2:153575800-153587200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:153575800-153611600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:153575800-153611600	Weak transcription	Esophagus	oesophagus
5	chr2:153575800-153621400	Weak transcription	Pancreas	Pancrea
6	chr2:153576000-153578400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr2:153576000-153579200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr2:153576000-153581200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr2:153576000-153594400	Weak transcription	Left Ventricle	heart
10	chr2:153576000-153615800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr2:153576200-153578400	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr2:153576200-153578400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr2:153576200-153578600	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr2:153576200-153594800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr2:153576600-153578400	Enhancers	Primary B cells from cord blood	blood
16	chr2:153576600-153587000	Weak transcription	Placenta	Placenta
17	chr2:153576800-153578800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr2:153576800-153581200	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr2:153576800-153581800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:153576800-153585200	Weak transcription	Fetal Stomach	stomach
21	chr2:153576800-153587200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr2:153576800-153591400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:153576800-153592600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr2:153576800-153592800	Weak transcription	NH-A	brain
25	chr2:153577000-153578600	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr2:153577000-153578800	Strong transcription	Fetal Muscle Trunk	muscle
27	chr2:153577000-153578800	Genic enhancers	HepG2	liver
28	chr2:153577000-153579200	Weak transcription	Right Ventricle	heart
29	chr2:153577000-153579400	Weak transcription	HMEC	breast
30	chr2:153577000-153582800	Weak transcription	Psoas Muscle	Psoas
31	chr2:153577000-153586400	Weak transcription	NHEK	skin
32	chr2:153577000-153587200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr2:153577000-153592600	Weak transcription	Fetal Intestine Large	intestine
34	chr2:153577000-153592800	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr2:153577000-153593000	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr2:153577000-153593000	Weak transcription	Osteobl	bone
37	chr2:153577000-153594400	Weak transcription	Aorta	Aorta
38	chr2:153577000-153594600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr2:153577000-153595000	Weak transcription	Stomach Smooth Muscle	stomach
40	chr2:153577200-153578400	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr2:153577200-153578400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr2:153577200-153578800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr2:153577200-153578800	Enhancers	Colon Smooth Muscle	Colon
44	chr2:153577200-153579000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr2:153577200-153579600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr2:153577200-153579800	Weak transcription	NHDF-Ad	bronchial
47	chr2:153577200-153580200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr2:153577200-153583600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr2:153577200-153584600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr2:153577200-153584800	Strong transcription	HUES48 Cell Line	embryonic stem cell

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