Variant report

Variant	rs408284
Chromosome Location	chr6:13282938-13282939
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:13280798..13285135-chr6:13573249..13575552,3	K562	blood:

Variant related genes	Relation type
ENSG00000124523	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs202067	0.86[CEU][hapmap]
rs366332	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs368590	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs393032	0.86[CEU][hapmap]
rs416831	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs426518	0.80[EUR][1000 genomes]
rs435466	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs449321	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];0.99[ASN][1000 genomes]
rs450025	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs452021	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs45450	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]
rs534266	0.80[EUR][1000 genomes]
rs546017	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs578290	0.85[AFR][1000 genomes]
rs617580	0.86[AFR][1000 genomes]
rs693758	0.81[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
rs408284	PHACTR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:83 , 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	chr6:13267400-13283600	Weak transcription	Fetal Brain Female	brain
3	chr6:13268000-13283600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr6:13269400-13284800	Weak transcription	Right Atrium	heart
5	chr6:13269600-13286600	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr6:13269600-13286600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr6:13270200-13291600	Weak transcription	HSMM	muscle
8	chr6:13270400-13285400	Weak transcription	Fetal Heart	heart
9	chr6:13270600-13283600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr6:13271600-13287200	Weak transcription	Fetal Lung	lung
11	chr6:13273000-13283600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr6:13273400-13286800	Weak transcription	Liver	Liver
13	chr6:13273800-13291400	Weak transcription	Psoas Muscle	Psoas
14	chr6:13274000-13283800	Weak transcription	Brain Substantia Nigra	brain
15	chr6:13274400-13286800	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr6:13274400-13287200	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr6:13274400-13289200	Weak transcription	HSMMtube	muscle
18	chr6:13274600-13286200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr6:13274600-13286800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr6:13274600-13302000	Weak transcription	Small Intestine	intestine
21	chr6:13274800-13286600	Weak transcription	Duodenum Mucosa	Duodenum
22	chr6:13274800-13287000	Weak transcription	Thymus	Thymus
23	chr6:13274800-13292800	Weak transcription	Colon Smooth Muscle	Colon
24	chr6:13275000-13285000	Weak transcription	Fetal Intestine Small	intestine
25	chr6:13275000-13286800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr6:13275000-13287000	Weak transcription	Gastric	stomach
27	chr6:13275200-13286400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr6:13275600-13286600	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr6:13275600-13287000	Weak transcription	Adipose Nuclei	Adipose
30	chr6:13275600-13291600	Weak transcription	Rectal Smooth Muscle	rectum
31	chr6:13276000-13287400	Genic enhancers	Primary B cells from peripheral blood	blood
32	chr6:13277400-13286200	Strong transcription	Stomach Smooth Muscle	stomach
33	chr6:13277400-13287000	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr6:13277600-13284200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr6:13277800-13285000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr6:13278800-13283600	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr6:13279000-13283600	Weak transcription	Brain Germinal Matrix	brain
38	chr6:13279200-13285400	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr6:13279200-13287000	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr6:13279400-13286800	Weak transcription	Fetal Intestine Large	intestine
41	chr6:13279400-13287800	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr6:13279600-13285400	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr6:13280000-13283600	Weak transcription	Brain Cingulate Gyrus	brain
44	chr6:13280000-13285000	Weak transcription	Brain Angular Gyrus	brain
45	chr6:13280000-13288000	Strong transcription	Brain Anterior Caudate	brain
46	chr6:13280000-13289000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr6:13280000-13292600	Weak transcription	NHLF	lung
48	chr6:13280200-13283800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr6:13280200-13285800	Strong transcription	Lung	lung
50	chr6:13280200-13292400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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