Variant report

Variant	rs45450
Chromosome Location	chr6:13285309-13285310
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:13284901-13290945	K562	blood:	n/a	n/a
2	POLR2A	chr6:13284875-13285957	GM12892	blood:	n/a	n/a
3	POLR2A	chr6:13284920-13285339	K562	blood:	n/a	n/a
4	POLR2A	chr6:13284889-13290972	GM12891	blood:	n/a	n/a
5	POLR2A	chr6:13285141-13285785	GM12891	blood:	n/a	n/a
6	POLR2A	chr6:13284773-13285948	GM12878	blood:	n/a	n/a
7	POLR2A	chr6:13284835-13292200	GM12878	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:13284272..13285779-chr6:13319081..13321274,2	K562	blood:
2	chr6:13284832..13286495-chr6:13306674..13309047,2	K562	blood:
3	chr6:13283735..13285772-chr6:13319081..13321268,2	K562	blood:
4	chr6:13284063..13286332-chr6:13306674..13308343,2	K562	blood:
5	chr6:13284401..13286648-chr6:13326821..13329047,2	MCF-7	breast:
6	chr6:13285089..13286893-chr6:13290326..13292618,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000215022	TF binding region
ENSG00000272379	Chromatin interaction
ENSG00000145979	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs17667989	0.85[CEU][hapmap]
rs202031	0.85[CEU][hapmap]
rs202037	0.82[CEU][hapmap]
rs202067	0.85[CEU][hapmap]
rs366332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs368590	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs393032	0.85[CEU][hapmap]
rs408284	1.00[CEU][hapmap];0.89[CHB][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs416831	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs417024	0.82[CEU][hapmap]
rs426518	0.80[EUR][1000 genomes]
rs435466	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs449321	1.00[CEU][hapmap];0.89[CHB][hapmap];0.81[JPT][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs450025	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs452021	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs534266	0.80[EUR][1000 genomes]
rs542618	0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs546017	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs578290	0.88[AFR][1000 genomes]
rs617580	0.86[AFR][1000 genomes]
rs693758	0.86[ASN][1000 genomes]
rs7763251	0.80[EUR][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	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1028533	chr6:13239059-13484814	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv538136	chr6:13239059-13484814	Strong transcription Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1034016	chr6:13248122-13418225	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS 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 miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs45450	PHACTR1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13249800-13287000	Weak transcription	Fetal Brain Male	brain
2	chr6:13269600-13286600	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr6:13269600-13286600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr6:13270200-13291600	Weak transcription	HSMM	muscle
5	chr6:13270400-13285400	Weak transcription	Fetal Heart	heart
6	chr6:13271600-13287200	Weak transcription	Fetal Lung	lung
7	chr6:13273400-13286800	Weak transcription	Liver	Liver
8	chr6:13273800-13291400	Weak transcription	Psoas Muscle	Psoas
9	chr6:13274400-13286800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr6:13274400-13287200	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr6:13274400-13289200	Weak transcription	HSMMtube	muscle
12	chr6:13274600-13286200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr6:13274600-13286800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr6:13274600-13302000	Weak transcription	Small Intestine	intestine
15	chr6:13274800-13286600	Weak transcription	Duodenum Mucosa	Duodenum
16	chr6:13274800-13287000	Weak transcription	Thymus	Thymus
17	chr6:13274800-13292800	Weak transcription	Colon Smooth Muscle	Colon
18	chr6:13275000-13286800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr6:13275000-13287000	Weak transcription	Gastric	stomach
20	chr6:13275200-13286400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr6:13275600-13286600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr6:13275600-13287000	Weak transcription	Adipose Nuclei	Adipose
23	chr6:13275600-13291600	Weak transcription	Rectal Smooth Muscle	rectum
24	chr6:13276000-13287400	Genic enhancers	Primary B cells from peripheral blood	blood
25	chr6:13277400-13286200	Strong transcription	Stomach Smooth Muscle	stomach
26	chr6:13277400-13287000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr6:13279200-13285400	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr6:13279200-13287000	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr6:13279400-13286800	Weak transcription	Fetal Intestine Large	intestine
30	chr6:13279400-13287800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr6:13279600-13285400	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr6:13280000-13288000	Strong transcription	Brain Anterior Caudate	brain
33	chr6:13280000-13289000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr6:13280000-13292600	Weak transcription	NHLF	lung
35	chr6:13280200-13285800	Strong transcription	Lung	lung
36	chr6:13280200-13292400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr6:13280800-13287000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr6:13280800-13287600	Weak transcription	NHDF-Ad	bronchial
39	chr6:13281200-13287000	Weak transcription	Primary T cells from cord blood	blood
40	chr6:13281400-13285600	Weak transcription	Fetal Thymus	thymus
41	chr6:13281400-13287000	Weak transcription	Placenta	Placenta
42	chr6:13281600-13285800	Strong transcription	Primary hematopoietic stem cells	blood
43	chr6:13281800-13286000	Strong transcription	Fetal Stomach	stomach
44	chr6:13281800-13286600	Strong transcription	K562	blood
45	chr6:13282400-13287000	Strong transcription	Left Ventricle	heart
46	chr6:13282800-13285600	Weak transcription	Ovary	ovary
47	chr6:13282800-13289400	Strong transcription	Right Ventricle	heart
48	chr6:13282800-13291600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr6:13283400-13287800	Strong transcription	Brain Hippocampus Middle	brain
50	chr6:13283600-13286000	Strong transcription	Brain Cingulate Gyrus	brain

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