Variant report

Variant	rs7874897
Chromosome Location	chr9:98695520-98695521
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	chr9:98686572..98689249-chr9:98695203..98698057,2	MCF-7	breast:
2	chr9:98692437..98694595-chr9:98695109..98697038,2	K562	blood:

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

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10121403	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10481647	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10739632	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10760675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10760692	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10818017	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10983692	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs10983739	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10983773	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10983818	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12004422	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12375861	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12553442	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1410783	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1928253	0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2117432	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2164156	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2164157	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs238	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs2770837	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3930253	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4743458	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs583716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs585223	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs591579	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs601916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs615866	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs617884	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs626264	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs631273	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs636456	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs640281	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs643815	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6478984	0.84[ASN][1000 genomes]
rs6479036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs676453	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs678244	1.00[CEU][hapmap]
rs680468	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs680754	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs683829	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs689627	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]
rs689749	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs689820	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs689871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs689979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs690222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs690304	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs690335	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs690420	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs690455	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs690484	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs700963	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7024710	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7028281	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7868559	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs816671	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs816676	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs816681	0.85[ASN][1000 genomes]
rs913408	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9409321	0.80[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9409322	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[ASN][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	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
2	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
3	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
rs7874897	LINC00476	cis	Nerve Tibial	GTEx
rs7874897	LINC00476	cis	Skin Sun Exposed Lower leg	GTEx
rs7874897	LINC00476	cis	Artery Aorta	GTEx
rs7874897	LINC00476	cis	Thyroid	GTEx
rs7874897	LINC00476	cis	lung	GTEx
rs7874897	LINC00476	cis	Stomach	GTEx
rs7874897	LINC00476	cis	Adipose Subcutaneous	GTEx
rs7874897	C9orf130	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98638800-98702200	Weak transcription	Pancreas	Pancrea
2	chr9:98640000-98718600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr9:98645800-98702200	Weak transcription	Aorta	Aorta
4	chr9:98649400-98718600	Weak transcription	Spleen	Spleen
5	chr9:98660000-98706000	Weak transcription	Fetal Heart	heart
6	chr9:98673600-98702200	Weak transcription	Small Intestine	intestine
7	chr9:98675400-98718600	Weak transcription	Esophagus	oesophagus
8	chr9:98677600-98709000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr9:98678000-98699200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr9:98678000-98699600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr9:98678600-98705600	Weak transcription	Psoas Muscle	Psoas
12	chr9:98678800-98718600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr9:98679400-98698600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr9:98680800-98706000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr9:98681800-98736600	Weak transcription	Colonic Mucosa	Colon
16	chr9:98682400-98698000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr9:98683200-98697800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr9:98683400-98702600	Strong transcription	HSMM	muscle
19	chr9:98684200-98697200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr9:98684800-98697800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr9:98685400-98699600	Strong transcription	Primary T cells from cord blood	blood
22	chr9:98685800-98698400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr9:98686000-98699200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr9:98686200-98699400	Weak transcription	NHEK	skin
25	chr9:98686400-98702200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr9:98686400-98709000	Weak transcription	Right Ventricle	heart
27	chr9:98686400-98711000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr9:98686400-98743800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr9:98686800-98696800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr9:98687200-98695800	Weak transcription	Brain Germinal Matrix	brain
31	chr9:98687800-98695800	Weak transcription	Thymus	Thymus
32	chr9:98687800-98697600	Weak transcription	Ovary	ovary
33	chr9:98687800-98700600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr9:98687800-98701800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr9:98687800-98703400	Weak transcription	Hela-S3	cervix
36	chr9:98687800-98709000	Weak transcription	Lung	lung
37	chr9:98687800-98718400	Weak transcription	Stomach Mucosa	stomach
38	chr9:98687800-98726000	Weak transcription	Gastric	stomach
39	chr9:98688400-98695800	Weak transcription	HUVEC	blood vessel
40	chr9:98688400-98699000	Weak transcription	Brain Substantia Nigra	brain
41	chr9:98688400-98702400	Strong transcription	HUES6 Cell Line	embryonic stem cell
42	chr9:98688600-98705800	Weak transcription	Colon Smooth Muscle	Colon
43	chr9:98688800-98703600	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr9:98689400-98700400	Strong transcription	Dnd41	blood
45	chr9:98689800-98697800	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr9:98689800-98700600	Strong transcription	Primary hematopoietic stem cells	blood
47	chr9:98689800-98703600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr9:98690000-98696200	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr9:98690000-98696400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr9:98690000-98698800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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