Variant report

Variant	rs11169284
Chromosome Location	chr12:50539764-50539765
allele	C/G
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	GATA3	chr12:50539586-50540219	MCF-7	breast:	n/a	chr12:50539895-50539902 chr12:50540010-50540018
2	GATA3	chr12:50539680-50540118	T-47D	breast:	n/a	chr12:50539895-50539902 chr12:50540010-50540018
3	GATA3	chr12:50539755-50540135	MCF-7	breast:	n/a	chr12:50539895-50539902 chr12:50540010-50540018

No.	Distal block	Cell Line	Cell type
1	chr12:50535984..50537611-chr12:50539393..50542341,2	K562	blood:
2	chr12:50529914..50531795-chr12:50537950..50540041,2	K562	blood:
3	chr12:50531935..50534070-chr12:50539130..50540855,2	K562	blood:
4	chr12:50478449..50481902-chr12:50536030..50539935,3	MCF-7	breast:
5	chr12:50497375..50499657-chr12:50539250..50540993,2	K562	blood:

Variant related genes	Relation type
CERS5	TF binding region
ENSG00000167588	Chromatin interaction
ENSG00000139624	Chromatin interaction
ENSG00000066117	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10735822	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10735823	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10747571	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10783336	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10783337	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10783339	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10783341	0.94[CHB][hapmap];0.89[JPT][hapmap];0.84[YRI][hapmap];0.85[ASN][1000 genomes]
rs10875999	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10876001	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10876002	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10876004	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10876006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10876007	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11169283	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11169285	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12229758	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12314572	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17124448	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1862044	0.87[CHB][hapmap];0.89[JPT][hapmap]
rs2008537	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2242507	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2277355	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55639096	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56151073	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7131794	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7297864	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7300549	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs7306213	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73106145	0.82[EUR][1000 genomes]
rs7314598	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7316344	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7486874	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7953174	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
4	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50517600-50548000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:50524000-50559800	Weak transcription	Right Atrium	heart
3	chr12:50524600-50541600	Weak transcription	Psoas Muscle	Psoas
4	chr12:50528800-50543000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr12:50529600-50542800	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr12:50529800-50543000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr12:50529800-50559800	Weak transcription	NHLF	lung
8	chr12:50530000-50559600	Weak transcription	A549	lung
9	chr12:50530000-50560200	Weak transcription	Esophagus	oesophagus
10	chr12:50531200-50548400	Weak transcription	HUVEC	blood vessel
11	chr12:50531600-50543200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr12:50531600-50558200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr12:50531800-50544600	Weak transcription	Fetal Kidney	kidney
14	chr12:50531800-50554400	Weak transcription	K562	blood
15	chr12:50531800-50558400	Weak transcription	Fetal Brain Male	brain
16	chr12:50532000-50560200	Weak transcription	Aorta	Aorta
17	chr12:50532000-50560200	Weak transcription	Gastric	stomach
18	chr12:50532400-50541200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr12:50532400-50541400	Weak transcription	Liver	Liver
20	chr12:50532400-50559800	Weak transcription	Spleen	Spleen
21	chr12:50532800-50542200	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr12:50533200-50544800	Weak transcription	Colon Smooth Muscle	Colon
23	chr12:50533200-50559400	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr12:50533400-50551200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr12:50534400-50560200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr12:50534600-50544800	Weak transcription	Ovary	ovary
27	chr12:50535000-50545400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr12:50535200-50541800	Weak transcription	Lung	lung
29	chr12:50535200-50545000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr12:50535200-50560000	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr12:50535200-50560200	Weak transcription	Right Ventricle	heart
32	chr12:50535400-50559400	Weak transcription	Duodenum Mucosa	Duodenum
33	chr12:50535400-50560000	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr12:50536400-50560200	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr12:50536800-50545000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr12:50537000-50539800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr12:50537000-50544600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr12:50537200-50558200	Weak transcription	Fetal Brain Female	brain
39	chr12:50537200-50559200	Weak transcription	Primary hematopoietic stem cells	blood
40	chr12:50537400-50543000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr12:50537400-50550600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr12:50537400-50559400	Weak transcription	Brain Hippocampus Middle	brain
43	chr12:50537400-50560200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr12:50537600-50559400	Weak transcription	Primary B cells from peripheral blood	blood
45	chr12:50537600-50559400	Weak transcription	Stomach Smooth Muscle	stomach
46	chr12:50537800-50544600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr12:50537800-50545000	Weak transcription	HMEC	breast
48	chr12:50537800-50545200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr12:50537800-50545200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr12:50537800-50547400	Weak transcription	Primary T cells from cord blood	blood

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