Variant report

Variant	rs617580
Chromosome Location	chr6:13286517-13286518
allele	A/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	SPI1	chr6:13286490-13286724	GM12878	blood:	n/a	chr6:13286612-13286625
2	BHLHE40	chr6:13286476-13286816	GM12878	blood:	n/a	n/a
3	SPI1	chr6:13286228-13287136	GM12878	blood:	n/a	chr6:13286612-13286625
4	MEF2A	chr6:13286380-13286757	GM12878	blood:	n/a	chr6:13286642-13286657
5	POLR2A	chr6:13284901-13290945	K562	blood:	n/a	n/a
6	SPI1	chr6:13286394-13286761	GM12878	blood:	n/a	chr6:13286612-13286625
7	SPI1	chr6:13286488-13286694	K562	blood:	n/a	chr6:13286612-13286625
8	POLR2A	chr6:13286513-13286629	GM12878	blood:	n/a	n/a
9	FOXM1	chr6:13286299-13286884	GM12878	blood:	n/a	n/a
10	SPI1	chr6:13285883-13286953	HL-60	blood:	n/a	chr6:13286612-13286625 chr6:13286130-13286143 chr6:13286134-13286141
11	MTA3	chr6:13286275-13286980	GM12878	blood:	n/a	n/a
12	IKZF1	chr6:13286409-13286770	GM12878	blood:	n/a	n/a
13	RUNX3	chr6:13286344-13286808	GM12878	blood:	n/a	n/a
14	NFIC	chr6:13286281-13286768	GM12878	blood:	n/a	n/a
15	POLR2A	chr6:13286472-13287355	GM12878	blood:	n/a	n/a
16	POLR2A	chr6:13285873-13286791	HL-60	blood:	n/a	n/a
17	POLR2A	chr6:13284889-13290972	GM12891	blood:	n/a	n/a
18	POLR2A	chr6:13284835-13292200	GM12878	blood:	n/a	n/a
19	SPI1	chr6:13286376-13286877	HL-60	blood:	n/a	chr6:13286612-13286625
20	SPI1	chr6:13286340-13286817	GM12891	blood:	n/a	chr6:13286612-13286625
21	SPI1	chr6:13286383-13286858	GM12891	blood:	n/a	chr6:13286612-13286625
22	POLR2A	chr6:13286475-13287398	GM12892	blood:	n/a	n/a
23	RUNX3	chr6:13286344-13286846	GM12878	blood:	n/a	n/a
24	E2F6	chr6:13286353-13286810	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr6:13286487-13286674	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:13281485..13284268-chr6:13286198..13288024,2	K562	blood:
2	chr6:13272685..13275870-chr6:13286064..13289898,4	K562	blood:
3	chr6:13284401..13286648-chr6:13326821..13329047,2	MCF-7	breast:
4	chr1:1508619..1510738-chr6:13285485..13287927,2	K562	blood:
5	chr6:13285089..13286893-chr6:13290326..13292618,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000215022	TF binding region
ENSG00000215014	Chromatin interaction
ENSG00000215022	Chromatin interaction
ENSG00000160075	Chromatin interaction
ENSG00000272379	Chromatin interaction
ENSG00000112137	Chromatin interaction
ENSG00000145979	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1223397	0.88[JPT][hapmap]
rs202016	0.82[EUR][1000 genomes]
rs202017	0.82[EUR][1000 genomes]
rs202018	0.83[CEU][hapmap];0.80[CHB][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes]
rs202019	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs202021	0.83[CEU][hapmap];0.80[CHB][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes]
rs202022	0.88[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs202023	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs202029	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs202032	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs20499	0.88[JPT][hapmap]
rs20500	0.88[JPT][hapmap]
rs2439534	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs2439537	0.88[CEU][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs2439539	0.83[CEU][hapmap];0.80[CHB][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes]
rs2439540	0.82[EUR][1000 genomes]
rs2439541	0.81[CEU][hapmap];0.84[CHB][hapmap];0.88[JPT][hapmap];0.82[EUR][1000 genomes]
rs2439542	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs2439545	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs2439548	0.82[CEU][hapmap];0.83[JPT][hapmap]
rs2458310	0.83[CEU][hapmap];0.80[CHB][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes]
rs2458311	0.83[CEU][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes]
rs2458312	0.83[CEU][hapmap];0.80[CHB][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes]
rs2458313	0.92[CEU][hapmap];0.83[CHB][hapmap];0.82[EUR][1000 genomes]
rs2458314	0.83[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2496140	0.83[CEU][hapmap];0.80[CHB][hapmap];0.83[JPT][hapmap];0.82[EUR][1000 genomes]
rs2496142	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs2496144	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs2496145	0.88[CEU][hapmap];0.82[JPT][hapmap]
rs2496147	0.83[CEU][hapmap];0.80[CHB][hapmap];0.83[JPT][hapmap]
rs2496148	0.83[CEU][hapmap];0.83[JPT][hapmap]
rs2496156	0.81[CEU][hapmap];0.83[CHB][hapmap];0.83[JPT][hapmap]
rs2496157	0.82[CEU][hapmap];0.82[JPT][hapmap]
rs364493	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs366332	0.86[AFR][1000 genomes]
rs368590	0.87[AFR][1000 genomes]
rs3817738	0.88[JPT][hapmap]
rs3817741	0.88[JPT][hapmap]
rs402705	0.88[CEU][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs408284	0.86[AFR][1000 genomes]
rs416831	0.86[AFR][1000 genomes]
rs435466	0.85[AFR][1000 genomes]
rs449321	0.86[AFR][1000 genomes]
rs449727	0.88[CEU][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs450025	0.86[AFR][1000 genomes]
rs452021	0.86[AFR][1000 genomes]
rs452309	0.82[EUR][1000 genomes]
rs453877	0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs45450	0.86[AFR][1000 genomes]
rs488297	0.81[EUR][1000 genomes]
rs546017	0.86[AFR][1000 genomes]
rs641758	0.88[CEU][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs9381884	0.88[JPT][hapmap]
rs9395602	0.88[JPT][hapmap]
rs9473901	0.81[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	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
rs617580	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	chr6:13271600-13287200	Weak transcription	Fetal Lung	lung
6	chr6:13273400-13286800	Weak transcription	Liver	Liver
7	chr6:13273800-13291400	Weak transcription	Psoas Muscle	Psoas
8	chr6:13274400-13286800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr6:13274400-13287200	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr6:13274400-13289200	Weak transcription	HSMMtube	muscle
11	chr6:13274600-13286800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr6:13274600-13302000	Weak transcription	Small Intestine	intestine
13	chr6:13274800-13286600	Weak transcription	Duodenum Mucosa	Duodenum
14	chr6:13274800-13287000	Weak transcription	Thymus	Thymus
15	chr6:13274800-13292800	Weak transcription	Colon Smooth Muscle	Colon
16	chr6:13275000-13286800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr6:13275000-13287000	Weak transcription	Gastric	stomach
18	chr6:13275600-13286600	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr6:13275600-13287000	Weak transcription	Adipose Nuclei	Adipose
20	chr6:13275600-13291600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr6:13276000-13287400	Genic enhancers	Primary B cells from peripheral blood	blood
22	chr6:13277400-13287000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr6:13279200-13287000	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr6:13279400-13286800	Weak transcription	Fetal Intestine Large	intestine
25	chr6:13279400-13287800	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr6:13280000-13288000	Strong transcription	Brain Anterior Caudate	brain
27	chr6:13280000-13289000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr6:13280000-13292600	Weak transcription	NHLF	lung
29	chr6:13280200-13292400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr6:13280800-13287000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr6:13280800-13287600	Weak transcription	NHDF-Ad	bronchial
32	chr6:13281200-13287000	Weak transcription	Primary T cells from cord blood	blood
33	chr6:13281400-13287000	Weak transcription	Placenta	Placenta
34	chr6:13281800-13286600	Strong transcription	K562	blood
35	chr6:13282400-13287000	Strong transcription	Left Ventricle	heart
36	chr6:13282800-13289400	Strong transcription	Right Ventricle	heart
37	chr6:13282800-13291600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr6:13283400-13287800	Strong transcription	Brain Hippocampus Middle	brain
39	chr6:13283600-13286800	Strong transcription	Fetal Brain Female	brain
40	chr6:13283600-13286800	Weak transcription	Fetal Muscle Trunk	muscle
41	chr6:13283600-13287000	Strong transcription	Brain Germinal Matrix	brain
42	chr6:13283600-13287200	Strong transcription	Brain Inferior Temporal Lobe	brain
43	chr6:13283600-13287400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr6:13283600-13287400	Strong transcription	Pancreas	Pancrea
45	chr6:13283600-13288600	Strong transcription	Aorta	Aorta
46	chr6:13283600-13289600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr6:13283800-13286600	Strong transcription	Fetal Muscle Leg	muscle
48	chr6:13284000-13286600	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr6:13284000-13293000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr6:13284000-13294200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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