Variant report

Variant	rs11504023
Chromosome Location	chr12:56505709-56505710
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	POLR2A	chr12:56505705-56506498	GM12891	blood:	n/a	n/a
2	POLR2A	chr12:56505583-56506964	GM12878	blood:	n/a	n/a
3	POLR2A	chr12:56505659-56506127	K562	blood:	n/a	n/a
4	POLR2A	chr12:56505695-56506929	GM12892	blood:	n/a	n/a
5	POLR2A	chr12:56505538-56506749	HepG2	liver:	n/a	n/a
6	POLR2A	chr12:56505559-56506332	SK-N-MC	brain:	n/a	n/a
7	POLR2A	chr12:56505632-56506997	GM12892	blood:	n/a	n/a
8	POLR2A	chr12:56505687-56505729	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:56471261..56483436-chr12:56494778..56506435,58	MCF-7	breast:
2	chr12:56433777..56443620-chr12:56502225..56514736,38	MCF-7	breast:

Variant related genes	Relation type
RPL41	TF binding region
ENSG00000257449	Chromatin interaction
ENSG00000065361	Chromatin interaction
ENSG00000197728	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11171746	0.83[AFR][1000 genomes]
rs11171754	0.83[AFR][1000 genomes]
rs11171755	0.83[AFR][1000 genomes]
rs12227040	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12296387	0.80[AFR][1000 genomes]
rs12298136	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12309692	0.83[AFR][1000 genomes]
rs17118317	0.90[ASN][1000 genomes]
rs28546848	0.89[AFR][1000 genomes]
rs28676339	0.83[AFR][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	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv1043988	chr12:56348185-56534900	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv832427	chr12:56392545-56512774	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	nsv973075	chr12:56500110-56507731	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56499200-56509600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:56499600-56505800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:56500000-56508200	Strong transcription	Fetal Muscle Trunk	muscle
4	chr12:56500200-56507600	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr12:56500200-56507600	Strong transcription	Psoas Muscle	Psoas
6	chr12:56500200-56507800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr12:56500200-56508000	Strong transcription	H9 Cell Line	embryonic stem cell
8	chr12:56500200-56508000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr12:56500200-56508200	Strong transcription	NH-A	brain
10	chr12:56500200-56508600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:56500400-56506400	Strong transcription	Colon Smooth Muscle	Colon
12	chr12:56500400-56506400	Strong transcription	NHLF	lung
13	chr12:56500400-56507200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr12:56500400-56507800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr12:56500400-56507800	Strong transcription	Muscle Satellite Cultured Cells	--
16	chr12:56500400-56507800	Strong transcription	Rectal Mucosa Donor 31	rectum
17	chr12:56500400-56507800	Strong transcription	Rectal Smooth Muscle	rectum
18	chr12:56500400-56507800	Strong transcription	Thymus	Thymus
19	chr12:56500400-56507800	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr12:56500400-56508000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr12:56500400-56508000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr12:56500400-56508000	Strong transcription	Fetal Muscle Leg	muscle
23	chr12:56500400-56508000	Strong transcription	Osteobl	bone
24	chr12:56500400-56508200	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr12:56500400-56508200	Strong transcription	Liver	Liver
26	chr12:56500400-56508400	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr12:56500400-56508400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr12:56500400-56508400	Strong transcription	Primary T cells from cord blood	blood
29	chr12:56500400-56508400	Strong transcription	Brain Hippocampus Middle	brain
30	chr12:56500400-56508400	Strong transcription	Duodenum Mucosa	Duodenum
31	chr12:56500400-56508400	Strong transcription	Skeletal Muscle Female	skeletal muscle
32	chr12:56500400-56509200	Weak transcription	Fetal Heart	heart
33	chr12:56500600-56506400	Strong transcription	Primary hematopoietic stem cells	blood
34	chr12:56500600-56506400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
35	chr12:56500600-56506600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
36	chr12:56500600-56506800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr12:56500600-56506800	Strong transcription	Brain Angular Gyrus	brain
38	chr12:56500600-56506800	Strong transcription	Brain Germinal Matrix	brain
39	chr12:56500600-56507000	Strong transcription	Colonic Mucosa	Colon
40	chr12:56500600-56507600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr12:56500600-56507600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr12:56500600-56507800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
43	chr12:56500600-56507800	Strong transcription	Brain Anterior Caudate	brain
44	chr12:56500600-56508000	Strong transcription	Primary B cells from peripheral blood	blood
45	chr12:56500600-56508000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr12:56500600-56508000	Strong transcription	Brain Substantia Nigra	brain
47	chr12:56500600-56508000	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr12:56500600-56508200	Strong transcription	HUES6 Cell Line	embryonic stem cell
49	chr12:56500600-56508200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr12:56500600-56508200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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