Variant report

Variant	rs6586899
Chromosome Location	chr8:20058757-20058758
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:20049831..20052925-chr8:20057041..20061103,3	K562	blood:
2	chr8:20053730..20056872-chr8:20057079..20060453,3	MCF-7	breast:
3	chr8:20058099..20059707-chr8:20060031..20061752,2	K562	blood:

Variant related genes	Relation type
ENSG00000147416	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs1106634	0.93[CEU][hapmap];0.81[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4921696	0.90[CEU][hapmap];0.93[JPT][hapmap]
rs4922139	0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv610759	chr8:19561997-20068842	Enhancers Strong transcription Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1033511	chr8:19751299-20625091	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv530877	chr8:19873053-20593254	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1015598	chr8:19963102-20088510	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv539523	chr8:19963102-20088510	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv6107	chr8:20056154-20100794	Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6586899	C11orf1	trans	parietal	SCAN
rs6586899	PDLIM2	cis	cerebellum	SCAN
rs6586899	IRF9	trans	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:20055400-20059200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr8:20056000-20059400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr8:20056000-20063800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr8:20056000-20066200	Weak transcription	Esophagus	oesophagus
5	chr8:20056200-20059400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr8:20056200-20060800	Weak transcription	Placenta	Placenta
7	chr8:20056200-20063000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr8:20056200-20063000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr8:20056200-20068200	Weak transcription	Colonic Mucosa	Colon
10	chr8:20056200-20072200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr8:20056400-20058800	Enhancers	Fetal Lung	lung
12	chr8:20056400-20059000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr8:20056400-20059400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr8:20056400-20059400	Weak transcription	Small Intestine	intestine
15	chr8:20056400-20060000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr8:20056400-20060600	Weak transcription	Right Ventricle	heart
17	chr8:20056400-20060800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr8:20056400-20061000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr8:20056400-20063600	Weak transcription	Primary B cells from peripheral blood	blood
20	chr8:20056400-20063800	Weak transcription	Fetal Stomach	stomach
21	chr8:20056400-20066400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr8:20056400-20066600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr8:20056400-20089600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr8:20056600-20059200	Weak transcription	Aorta	Aorta
25	chr8:20056600-20061400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr8:20056600-20063800	Weak transcription	Fetal Muscle Leg	muscle
27	chr8:20056800-20059000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr8:20056800-20059200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr8:20056800-20059600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr8:20056800-20060200	Weak transcription	Brain Substantia Nigra	brain
31	chr8:20056800-20060600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr8:20056800-20063600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr8:20056800-20066400	Weak transcription	Fetal Kidney	kidney
34	chr8:20057000-20058800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr8:20057000-20058800	Weak transcription	HSMMtube	muscle
36	chr8:20057000-20059400	Weak transcription	Brain Cingulate Gyrus	brain
37	chr8:20057000-20059400	Weak transcription	HUVEC	blood vessel
38	chr8:20057000-20059400	Weak transcription	NH-A	brain
39	chr8:20057000-20059600	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr8:20057000-20059800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr8:20057000-20060800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr8:20057000-20061400	Enhancers	Adipose Nuclei	Adipose
43	chr8:20057000-20061800	Enhancers	Primary T helper cells PMA-I stimulated	--
44	chr8:20057000-20063600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr8:20057000-20063600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr8:20057000-20066400	Weak transcription	Thymus	Thymus
47	chr8:20057000-20066600	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr8:20057000-20066600	Weak transcription	Stomach Smooth Muscle	stomach
49	chr8:20057000-20066800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr8:20057000-20066800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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