Variant report

Variant	rs689627
Chromosome Location	chr9:98663600-98663601
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:98659421..98661282-chr9:98663215..98665400,2	MCF-7	breast:
2	chr9:98663269..98664821-chr9:98672386..98673903,2	K562	blood:
3	chr9:98637758..98639724-chr9:98662859..98665137,2	K562	blood:

Variant related genes	Relation type
ENSG00000175611	Chromatin interaction
ENSG00000182150	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10121403	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10481647	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10739632	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10760675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10760692	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10818017	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10983622	0.81[CHB][hapmap]
rs10983692	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs10983739	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs10983773	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs10983818	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12004422	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12375861	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12553442	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1410783	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1928253	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2117432	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2164156	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2164157	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs238	0.96[CEU][hapmap]
rs3930253	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4743458	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs583716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs585223	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs591579	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs601916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs615866	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs617884	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs626264	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs631273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs636456	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs640281	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs643815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6479036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs676453	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs678244	1.00[CEU][hapmap]
rs680468	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs680754	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs683829	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs689749	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs689820	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs689871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs689979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs690222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs690304	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs690335	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs690420	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs690455	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs690484	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs700963	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs7024710	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7028281	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7868559	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7874897	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs816671	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs816676	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs913408	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9409321	0.80[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap]
rs9409322	0.93[CHB][hapmap];1.00[JPT][hapmap]

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	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
4	esv1801890	chr9:98660433-98701801	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs689627	C9orf130	cis	brain	BrainEAC
rs689627	LINC00476	cis	Thyroid	GTEx
rs689627	LINC00476	cis	lung	GTEx
rs689627	C9orf130	Cis_1M	lymphoblastoid	RTeQTL
rs689627	LINC00476	cis	Adipose Subcutaneous	GTEx
rs689627	LINC00476	cis	Nerve Tibial	GTEx
rs689627	LINC00476	cis	Artery Aorta	GTEx
rs689627	C9orf130	cis	intralobular white matter	BrainEAC

Chromatin state (count:119 , 50 per page) page: 1 2 3

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	chr9:98640000-98663600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr9:98640000-98678200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr9:98640000-98680600	Weak transcription	Colonic Mucosa	Colon
10	chr9:98640000-98685600	Weak transcription	Right Ventricle	heart
11	chr9:98640000-98718600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr9:98640200-98678200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr9:98640400-98664800	Weak transcription	Brain Substantia Nigra	brain
14	chr9:98640400-98677800	Weak transcription	Psoas Muscle	Psoas
15	chr9:98640600-98678000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr9:98642200-98663600	Weak transcription	Hela-S3	cervix
17	chr9:98642600-98678000	Weak transcription	Colon Smooth Muscle	Colon
18	chr9:98642600-98680600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr9:98642800-98668200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr9:98642800-98681800	Weak transcription	Fetal Kidney	kidney
21	chr9:98644200-98670600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr9:98644400-98678400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr9:98644400-98685600	Weak transcription	Gastric	stomach
24	chr9:98644600-98670200	Weak transcription	Left Ventricle	heart
25	chr9:98644600-98678000	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr9:98644600-98690800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr9:98644800-98677400	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr9:98645600-98684200	Weak transcription	Brain Hippocampus Middle	brain
29	chr9:98645800-98670400	Weak transcription	Brain Germinal Matrix	brain
30	chr9:98645800-98672600	Weak transcription	HUVEC	blood vessel
31	chr9:98645800-98678400	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr9:98645800-98702200	Weak transcription	Aorta	Aorta
33	chr9:98646000-98680200	Weak transcription	K562	blood
34	chr9:98646400-98663800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr9:98646600-98667800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr9:98646600-98670000	Weak transcription	Adipose Nuclei	Adipose
37	chr9:98646600-98681800	Weak transcription	HSMMtube	muscle
38	chr9:98646800-98672400	Weak transcription	NHDF-Ad	bronchial
39	chr9:98647400-98672800	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr9:98647600-98678000	Weak transcription	Stomach Smooth Muscle	stomach
41	chr9:98647800-98677400	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr9:98648200-98666200	Weak transcription	HSMM	muscle
43	chr9:98648200-98677800	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr9:98648200-98678600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr9:98649000-98667800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr9:98649200-98670000	Weak transcription	Fetal Muscle Trunk	muscle
47	chr9:98649400-98670200	Weak transcription	Fetal Lung	lung
48	chr9:98649400-98676000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr9:98649400-98694400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr9:98649400-98718600	Weak transcription	Spleen	Spleen

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