Variant report

Variant	rs6884579
Chromosome Location	chr5:89686946-89686947
allele	A/C
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	chr5:89686462-89687744	K562	blood:	n/a	n/a
2	TEAD4	chr5:89686750-89687032	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:89686339..89688642-chr5:89694620..89696372,2	K562	blood:
2	chr5:89680507..89687450-chr5:89698366..89705754,8	MCF-7	breast:
3	chr5:89684756..89687141-chr5:89703504..89706860,3	MCF-7	breast:
4	chr5:89680611..89687152-chr5:89704124..89707534,9	K562	blood:

Variant related genes	Relation type
ENSG00000260871	TF binding region
ENSG00000153140	Chromatin interaction
ENSG00000255647	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10054133	0.89[EUR][1000 genomes]
rs10474325	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11744529	0.91[CEU][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11953190	0.90[EUR][1000 genomes]
rs11958751	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2115501	0.86[ASW][hapmap];0.91[CEU][hapmap];0.83[MKK][hapmap];0.80[YRI][hapmap];0.88[EUR][1000 genomes]
rs2963695	0.83[EUR][1000 genomes]
rs2972966	0.84[CEU][hapmap];0.92[EUR][1000 genomes]
rs4129345	0.84[CEU][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes]
rs4131978	0.93[EUR][1000 genomes]
rs57443165	0.88[EUR][1000 genomes]
rs72781070	0.93[EUR][1000 genomes]
rs72781074	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021142	chr5:89102893-89897826	Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv537804	chr5:89102893-89897826	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv917025	chr5:89208994-89855436	Enhancers Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv432750	chr5:89410113-90137144	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv432751	chr5:89457044-90090444	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
7	nsv882363	chr5:89643399-89725515	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6884579	POLR3G	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:89677000-89688400	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr5:89679600-89689600	Weak transcription	HepG2	liver
3	chr5:89679800-89688200	Weak transcription	Liver	Liver
4	chr5:89681600-89704600	Weak transcription	Aorta	Aorta
5	chr5:89683000-89694200	Weak transcription	Fetal Intestine Large	intestine
6	chr5:89683400-89688400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr5:89683400-89703800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr5:89683600-89697600	Weak transcription	Left Ventricle	heart
9	chr5:89684400-89693400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr5:89685400-89688200	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr5:89686000-89704400	Weak transcription	Psoas Muscle	Psoas
12	chr5:89686200-89694000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr5:89686400-89687200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr5:89686400-89687800	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr5:89686400-89688200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr5:89686400-89688200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr5:89686400-89694200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr5:89686400-89704400	Weak transcription	Small Intestine	intestine
19	chr5:89686600-89687000	Enhancers	Fetal Lung	lung
20	chr5:89686600-89687200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr5:89686600-89687200	Enhancers	H9 Cell Line	embryonic stem cell
22	chr5:89686600-89687200	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr5:89686600-89687400	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr5:89686600-89687600	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr5:89686600-89687600	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr5:89686600-89688200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr5:89686600-89688200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr5:89686600-89688200	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr5:89686600-89689000	Weak transcription	Dnd41	blood
30	chr5:89686600-89690800	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr5:89686600-89693400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr5:89686600-89693800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr5:89686600-89694600	Weak transcription	Primary T cells from cord blood	blood
34	chr5:89686600-89704200	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr5:89686800-89687000	Enhancers	H1 Cell Line	embryonic stem cell
36	chr5:89686800-89687000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr5:89686800-89687000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr5:89686800-89687000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr5:89686800-89687200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr5:89686800-89687400	Enhancers	HUES48 Cell Line	embryonic stem cell
41	chr5:89686800-89688200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr5:89686800-89688400	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr5:89686800-89688400	Weak transcription	Adipose Nuclei	Adipose
44	chr5:89686800-89688400	Weak transcription	GM12878-XiMat	blood
45	chr5:89686800-89688400	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr5:89686800-89692800	Weak transcription	Primary B cells from peripheral blood	blood
47	chr5:89686800-89693400	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr5:89686800-89693800	Weak transcription	Brain Hippocampus Middle	brain
49	chr5:89686800-89694200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr5:89686800-89704400	Weak transcription	Fetal Kidney	kidney

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