Variant report

Variant	rs690563
Chromosome Location	chr9:98634445-98634446
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	CEBPB	chr9:98634416-98634630	K562	blood:	n/a	chr9:98634532-98634543
2	POLR2A	chr9:98634018-98634710	K562	blood:	n/a	n/a
3	CEBPB	chr9:98634417-98634669	HepG2	liver:	n/a	chr9:98634532-98634543

No.	Distal block	Cell Line	Cell type
1	chr9:98614433..98624477-chr9:98629889..98639636,23	MCF-7	breast:
2	chr9:98624670..98626766-chr9:98633478..98635523,2	K562	blood:
3	chr9:98266714..98268433-chr9:98632145..98634773,2	MCF-7	breast:

Variant related genes	Relation type
ERCC6L2	TF binding region
ENSG00000252847	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10739787	0.92[CEU][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1410783	0.92[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs591579	0.96[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs667018	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs683829	0.92[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7865593	0.92[CEU][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs816671	0.85[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs816681	0.81[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	nsv893598	chr9:98508628-98645674	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv482884	chr9:98530027-98691937	Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
3	nsv893599	chr9:98542410-98991254	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv893600	chr9:98608989-98775459	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs690563	LINC00476	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98602000-98636000	Weak transcription	Lung	lung
2	chr9:98610200-98636200	Weak transcription	Brain Germinal Matrix	brain
3	chr9:98610200-98636800	Weak transcription	Gastric	stomach
4	chr9:98620400-98636200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr9:98620600-98636600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr9:98621000-98636400	Weak transcription	Hela-S3	cervix
7	chr9:98624600-98636400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr9:98625000-98636200	Weak transcription	Fetal Lung	lung
9	chr9:98626200-98636400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr9:98627200-98634800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr9:98628000-98636400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr9:98628200-98636200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr9:98628400-98636800	Weak transcription	Thymus	Thymus
14	chr9:98629200-98636600	Weak transcription	Primary B cells from cord blood	blood
15	chr9:98630200-98636200	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr9:98630400-98636600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr9:98630600-98636200	Weak transcription	Brain Anterior Caudate	brain
18	chr9:98630600-98636400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr9:98630800-98634600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr9:98631200-98636000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr9:98631200-98636600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr9:98631200-98636600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr9:98631200-98636600	Weak transcription	NH-A	brain
24	chr9:98631400-98636400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr9:98631400-98636600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr9:98631400-98636600	Weak transcription	Osteobl	bone
27	chr9:98631800-98636400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr9:98631800-98636400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr9:98631800-98636800	Weak transcription	Ovary	ovary
30	chr9:98632000-98636800	Weak transcription	Esophagus	oesophagus
31	chr9:98632200-98636400	Weak transcription	Fetal Intestine Small	intestine
32	chr9:98632200-98636600	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr9:98632400-98636800	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr9:98632600-98636000	Weak transcription	Brain Hippocampus Middle	brain
35	chr9:98632600-98636600	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr9:98632800-98634800	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr9:98632800-98635400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr9:98632800-98636400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr9:98632800-98636800	Weak transcription	Placenta	Placenta
40	chr9:98632800-98636800	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr9:98633000-98634800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr9:98633000-98636000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr9:98633000-98636600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr9:98633000-98636800	Weak transcription	HSMMtube	muscle
45	chr9:98633200-98635800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr9:98633200-98636200	Weak transcription	Stomach Smooth Muscle	stomach
47	chr9:98633200-98636400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr9:98633200-98636400	Weak transcription	HMEC	breast
49	chr9:98633200-98636600	Weak transcription	Adipose Nuclei	Adipose
50	chr9:98633200-98636800	Weak transcription	Fetal Thymus	thymus

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