Variant report

Variant	rs4768087
Chromosome Location	chr12:45678953-45678954
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:45668515..45671060-chr12:45676704..45679676,2	K562	blood:
2	chr12:45625766..45629467-chr12:45675676..45680562,5	MCF-7	breast:
3	chr12:45677746..45679951-chr12:45681323..45682867,2	K562	blood:
4	chr12:45677743..45680287-chr12:45681430..45684437,3	MCF-7	breast:
5	chr12:45608418..45611765-chr12:45675004..45680451,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177119	Chromatin interaction
ENSG00000134297	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1004598	0.88[AFR][1000 genomes]
rs1019584	0.83[AFR][1000 genomes]
rs1025088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10492285	1.00[CEU][hapmap];0.83[CHB][hapmap]
rs10736024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10748416	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10748417	0.81[AFR][1000 genomes]
rs10748418	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10748420	0.81[YRI][hapmap];0.86[AFR][1000 genomes]
rs10785559	0.83[AFR][1000 genomes]
rs10785564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10785565	0.86[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10785568	0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10880773	0.87[AFR][1000 genomes]
rs11182971	0.83[AMR][1000 genomes]
rs11182980	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1238407	0.83[AFR][1000 genomes]
rs12578188	1.00[CEU][hapmap]
rs12578220	1.00[CEU][hapmap]
rs12578314	1.00[CEU][hapmap];0.84[CHB][hapmap]
rs12579080	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12580320	1.00[CEU][hapmap]
rs12581525	1.00[CEU][hapmap]
rs12581554	1.00[CEU][hapmap]
rs12582025	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12582369	1.00[CEU][hapmap];0.83[CHB][hapmap]
rs17095441	1.00[CEU][hapmap]
rs17095584	1.00[CEU][hapmap];0.83[CHB][hapmap]
rs17095688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17095706	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17095713	1.00[CEU][hapmap]
rs17095716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17095721	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17095722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17095723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17095736	1.00[CEU][hapmap];0.92[JPT][hapmap]
rs17095784	1.00[CEU][hapmap]
rs17095866	1.00[CEU][hapmap]
rs17095888	1.00[CEU][hapmap]
rs17095911	1.00[CEU][hapmap]
rs1862907	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs1877972	0.83[AMR][1000 genomes]
rs1896027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1913691	0.81[YRI][hapmap];0.86[AFR][1000 genomes]
rs2037855	0.81[YRI][hapmap];0.90[AFR][1000 genomes]
rs2037856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2037857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3920257	1.00[CEU][hapmap]
rs41331147	1.00[CEU][hapmap];0.83[CHB][hapmap]
rs4489808	0.87[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4768600	1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4768604	0.83[AMR][1000 genomes]
rs4768605	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4768606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6582542	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6582543	0.83[AMR][1000 genomes]
rs7135029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7136281	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7304389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs7304749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7486228	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7953360	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7960422	0.91[AFR][1000 genomes]
rs7970250	0.80[YRI][hapmap];0.88[AFR][1000 genomes]
rs7970619	0.83[AMR][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	nsv1050923	chr12:45581310-45808289	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv690	chr12:45674127-45718859	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45654400-45725600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr12:45662800-45685400	Weak transcription	Primary B cells from peripheral blood	blood
3	chr12:45662800-45696800	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr12:45663400-45680400	Weak transcription	GM12878-XiMat	blood
5	chr12:45666200-45709200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr12:45668400-45697800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr12:45668600-45679200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr12:45668600-45693000	Weak transcription	Pancreas	Pancrea
9	chr12:45670200-45680600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:45674200-45680400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr12:45674200-45706800	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr12:45674400-45679000	Weak transcription	Aorta	Aorta
13	chr12:45674400-45692200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:45674600-45686400	Weak transcription	K562	blood
15	chr12:45675000-45680600	Weak transcription	Primary hematopoietic stem cells	blood
16	chr12:45675200-45680200	Enhancers	Fetal Intestine Large	intestine
17	chr12:45675400-45679000	Enhancers	Duodenum Mucosa	Duodenum
18	chr12:45675600-45680200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr12:45675800-45709000	Weak transcription	Lung	lung
20	chr12:45676000-45679200	Weak transcription	Left Ventricle	heart
21	chr12:45676000-45686600	Weak transcription	Right Atrium	heart
22	chr12:45676200-45693000	Weak transcription	Fetal Stomach	stomach
23	chr12:45676400-45685600	Weak transcription	Primary B cells from cord blood	blood
24	chr12:45676400-45696000	Weak transcription	Fetal Thymus	thymus
25	chr12:45676400-45697800	Weak transcription	Dnd41	blood
26	chr12:45676400-45740400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr12:45676600-45679600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr12:45677000-45679000	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr12:45677000-45679200	Enhancers	HMEC	breast
30	chr12:45677000-45679400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr12:45677000-45680000	Enhancers	Placenta Amnion	Placenta Amnion
32	chr12:45677000-45689800	Weak transcription	Liver	Liver
33	chr12:45677000-45696000	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr12:45677200-45679200	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr12:45677200-45679200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr12:45677200-45679200	Enhancers	NHDF-Ad	bronchial
37	chr12:45677200-45679800	Enhancers	NH-A	brain
38	chr12:45677200-45680200	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr12:45677200-45680800	Enhancers	Placenta	Placenta
40	chr12:45677400-45679000	Flanking Active TSS	A549	lung
41	chr12:45677400-45679200	Enhancers	Muscle Satellite Cultured Cells	--
42	chr12:45677400-45679400	Enhancers	Hela-S3	cervix
43	chr12:45677400-45681200	Enhancers	Colon Smooth Muscle	Colon
44	chr12:45677600-45679000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr12:45677600-45679000	Enhancers	Fetal Kidney	kidney
46	chr12:45677600-45679200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr12:45677600-45679200	Enhancers	Fetal Heart	heart
48	chr12:45677600-45679400	Enhancers	NHLF	lung
49	chr12:45677600-45698200	Weak transcription	Primary T cells from cord blood	blood
50	chr12:45677800-45679000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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