Variant report

Variant	rs10121403
Chromosome Location	chr9:98631875-98631876
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:98627050..98630496-chr9:98631101..98634293,4	K562	blood:
2	chr9:98631788..98634188-chr9:98659492..98662197,2	K562	blood:
3	chr9:98562023..98564379-chr9:98630316..98632934,2	MCF-7	breast:
4	chr9:98614433..98624477-chr9:98629889..98639636,23	MCF-7	breast:
5	chr3:143689788..143691376-chr9:98631114..98634044,2	MCF-7	breast:
6	chr9:98629164..98632859-chr9:98633356..98639163,9	K562	blood:
7	chr9:98626986..98632585-chr9:98632790..98639988,21	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182150	Chromatin interaction
ENSG00000175611	Chromatin interaction
ENSG00000181744	Chromatin interaction
ENSG00000252847	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10481647	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10739632	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10760675	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10760692	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10818017	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10983622	0.82[EUR][1000 genomes]
rs10983692	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10983739	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10983773	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10983818	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12004422	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12375861	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12553442	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1410783	0.99[ASN][1000 genomes]
rs1928253	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2117432	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2164156	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2164157	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2770837	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3930253	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4743458	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs583716	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs585223	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs591579	1.00[ASN][1000 genomes]
rs601916	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs615866	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs617884	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs626264	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs631273	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs636456	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs640281	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs643815	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6478984	0.84[ASN][1000 genomes]
rs6479036	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs676453	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs680468	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs680754	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs683829	0.99[ASN][1000 genomes]
rs689627	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs689749	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs689820	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs689871	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs689979	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs690222	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs690304	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs690335	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs690420	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs690455	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs690484	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs700963	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7024710	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7028281	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7868559	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7874897	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs816671	0.86[ASN][1000 genomes]
rs816676	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs816681	0.86[ASN][1000 genomes]
rs913408	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9409321	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9409322	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs10121403	LINC00476	cis	Adipose Subcutaneous	GTEx
rs10121403	LINC00476	cis	Skin Sun Exposed Lower leg	GTEx
rs10121403	LINC00476	cis	lung	GTEx
rs10121403	LINC00476	cis	Artery Aorta	GTEx
rs10121403	LINC00476	cis	Thyroid	GTEx
rs10121403	LINC00476	cis	Stomach	GTEx
rs10121403	C9orf130	Cis_1M	lymphoblastoid	RTeQTL
rs10121403	LINC00476	cis	Nerve Tibial	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98602000-98632800	Weak transcription	Left Ventricle	heart
2	chr9:98602000-98636000	Weak transcription	Lung	lung
3	chr9:98610200-98636200	Weak transcription	Brain Germinal Matrix	brain
4	chr9:98610200-98636800	Weak transcription	Gastric	stomach
5	chr9:98613400-98632800	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr9:98617000-98634200	Weak transcription	Fetal Kidney	kidney
7	chr9:98619800-98633000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr9:98619800-98633800	Weak transcription	Colon Smooth Muscle	Colon
9	chr9:98620400-98636200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr9:98620600-98636600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr9:98621000-98636400	Weak transcription	Hela-S3	cervix
12	chr9:98624600-98636400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr9:98625000-98636200	Weak transcription	Fetal Lung	lung
14	chr9:98625200-98632000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr9:98625400-98634400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr9:98625800-98634400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr9:98626200-98636400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr9:98626800-98632400	Weak transcription	Primary hematopoietic stem cells	blood
19	chr9:98627200-98634800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr9:98628000-98636400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr9:98628200-98636200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr9:98628400-98636800	Weak transcription	Thymus	Thymus
23	chr9:98629200-98636600	Weak transcription	Primary B cells from cord blood	blood
24	chr9:98630000-98634200	Weak transcription	HSMM	muscle
25	chr9:98630200-98634200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr9:98630200-98636200	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr9:98630400-98636600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr9:98630600-98636200	Weak transcription	Brain Anterior Caudate	brain
29	chr9:98630600-98636400	Weak transcription	Rectal Smooth Muscle	rectum
30	chr9:98630800-98634600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr9:98631000-98632800	Weak transcription	Adipose Nuclei	Adipose
32	chr9:98631000-98634200	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr9:98631200-98632400	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr9:98631200-98636000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr9:98631200-98636600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr9:98631200-98636600	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr9:98631200-98636600	Weak transcription	NH-A	brain
38	chr9:98631400-98636400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr9:98631400-98636600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr9:98631400-98636600	Weak transcription	Osteobl	bone
41	chr9:98631600-98633200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr9:98631600-98633400	Strong transcription	Liver	Liver
43	chr9:98631800-98632000	ZNF genes & repeats	Esophagus	oesophagus
44	chr9:98631800-98632200	ZNF genes & repeats	Fetal Intestine Small	intestine
45	chr9:98631800-98636400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr9:98631800-98636400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr9:98631800-98636800	Weak transcription	Ovary	ovary

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