Variant report

Variant	rs12683310
Chromosome Location	chr9:98655313-98655314
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:98654370..98657235-chr9:98658443..98661205,2	K562	blood:
2	chr9:98637241..98639130-chr9:98654520..98657385,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182150	Chromatin interaction
ENSG00000175611	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10988792	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10988804	0.94[YRI][hapmap];0.90[AFR][1000 genomes]
rs11787559	0.99[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12001	0.91[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12685221	0.82[EUR][1000 genomes]
rs12685318	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12685807	0.91[CEU][hapmap];0.92[CHB][hapmap];0.94[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1360064	0.81[EUR][1000 genomes]
rs16910298	0.83[EUR][1000 genomes]
rs1831228	0.82[EUR][1000 genomes]
rs2026032	0.80[YRI][hapmap];0.96[AFR][1000 genomes]
rs2069053	0.83[EUR][1000 genomes]
rs2274653	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2274654	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3802438	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4742781	0.82[EUR][1000 genomes]
rs4743391	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743400	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743417	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4743419	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7868270	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12683310	C9orf130	cis	lesional skin	skin_eQTL
rs12683310	LINC00476	cis	Esophagus Mucosa	GTEx
rs12683310	LINC00476	cis	Whole Blood	GTEx
rs12683310	C9orf130	Cis_1M	lymphoblastoid	RTeQTL
rs12683310	LINC00476	cis	Esophagus Muscularis	GTEx
rs12683310	LINC00476	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98638800-98702200	Weak transcription	Pancreas	Pancrea
2	chr9:98639400-98677800	Weak transcription	Placenta	Placenta
3	chr9:98639400-98678000	Weak transcription	Ovary	ovary
4	chr9:98639600-98678000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr9:98639800-98664200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr9:98639800-98677800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr9:98640000-98661600	Weak transcription	Right Atrium	heart
8	chr9:98640000-98663600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr9:98640000-98678200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr9:98640000-98680600	Weak transcription	Colonic Mucosa	Colon
11	chr9:98640000-98685600	Weak transcription	Right Ventricle	heart
12	chr9:98640000-98718600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr9:98640200-98678200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr9:98640400-98664800	Weak transcription	Brain Substantia Nigra	brain
15	chr9:98640400-98677800	Weak transcription	Psoas Muscle	Psoas
16	chr9:98640600-98678000	Weak transcription	Brain Cingulate Gyrus	brain
17	chr9:98642200-98663600	Weak transcription	Hela-S3	cervix
18	chr9:98642600-98678000	Weak transcription	Colon Smooth Muscle	Colon
19	chr9:98642600-98680600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr9:98642800-98668200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr9:98642800-98681800	Weak transcription	Fetal Kidney	kidney
22	chr9:98644200-98670600	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr9:98644400-98678400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr9:98644400-98685600	Weak transcription	Gastric	stomach
25	chr9:98644600-98670200	Weak transcription	Left Ventricle	heart
26	chr9:98644600-98678000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr9:98644600-98690800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr9:98644800-98677400	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr9:98645000-98662400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr9:98645600-98684200	Weak transcription	Brain Hippocampus Middle	brain
31	chr9:98645800-98670400	Weak transcription	Brain Germinal Matrix	brain
32	chr9:98645800-98672600	Weak transcription	HUVEC	blood vessel
33	chr9:98645800-98678400	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr9:98645800-98702200	Weak transcription	Aorta	Aorta
35	chr9:98646000-98680200	Weak transcription	K562	blood
36	chr9:98646400-98663800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr9:98646600-98667800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr9:98646600-98670000	Weak transcription	Adipose Nuclei	Adipose
39	chr9:98646600-98681800	Weak transcription	HSMMtube	muscle
40	chr9:98646800-98672400	Weak transcription	NHDF-Ad	bronchial
41	chr9:98647400-98672800	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr9:98647600-98661600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr9:98647600-98678000	Weak transcription	Stomach Smooth Muscle	stomach
44	chr9:98647800-98677400	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr9:98648200-98660000	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr9:98648200-98660800	Weak transcription	HepG2	liver
47	chr9:98648200-98662000	Weak transcription	Duodenum Mucosa	Duodenum
48	chr9:98648200-98666200	Weak transcription	HSMM	muscle
49	chr9:98648200-98677800	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr9:98648200-98678600	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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