Variant report

Variant	rs596413
Chromosome Location	chr9:98633843-98633844
allele	G/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	chr9:98614433..98624477-chr9:98629889..98639636,23	MCF-7	breast:
4	chr3:143689788..143691376-chr9:98631114..98634044,2	MCF-7	breast:
5	chr9:98624670..98626766-chr9:98633478..98635523,2	K562	blood:
6	chr9:98266714..98268433-chr9:98632145..98634773,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000181744	Chromatin interaction
ENSG00000252847	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10115110	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10117340	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10125109	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10512242	0.85[AMR][1000 genomes]
rs10512245	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10739622	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10739705	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10760189	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10760261	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10760262	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10760269	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10760679	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10818574	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10818746	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10818899	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10819650	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10819663	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10819668	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10819720	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10985156	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10985499	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10985769	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10987963	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10988755	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10988817	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10989035	0.88[AMR][1000 genomes]
rs1195130	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11998982	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12000073	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12340954	0.87[AMR][1000 genomes]
rs12343734	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12345187	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12347675	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12348051	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12349742	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1327996	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1327997	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13289466	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13294931	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13298093	0.85[AMR][1000 genomes]
rs13299166	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2026031	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2296858	0.94[AMR][1000 genomes]
rs2405134	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2405371	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2405372	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2943532	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs589362	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs603947	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs609296	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs617187	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs623438	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs624075	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs625105	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62559026	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62559767	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs640297	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6478977	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs649819	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs657451	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs666093	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs667705	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs671058	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs682682	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs684455	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs686048	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs689619	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs689696	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs689697	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs689710	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs689738	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs689744	0.94[AMR][1000 genomes]
rs689761	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs689804	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs689860	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs689911	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs689986	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs690056	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs690063	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs690286	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs690495	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs690528	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs690633	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs694230	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs700962	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7847393	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7847983	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7852346	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7871709	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs816670	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs816672	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs816673	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs816674	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs816675	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs816678	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs816680	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs816682	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs816683	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs816684	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs966217	1.00[AMR][1000 genomes];0.95[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs596413	ERCC6L2	cis	Artery Tibial	GTEx
rs596413	C9orf102	cis	multi-tissue	Pritchard
rs596413	C9orf130	Cis_1M	lymphoblastoid	RTeQTL
rs596413	ERCC6L2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:82 , 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	chr9:98617000-98634200	Weak transcription	Fetal Kidney	kidney
5	chr9:98620400-98636200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr9:98620600-98636600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr9:98621000-98636400	Weak transcription	Hela-S3	cervix
8	chr9:98624600-98636400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr9:98625000-98636200	Weak transcription	Fetal Lung	lung
10	chr9:98625400-98634400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr9:98625800-98634400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr9:98626200-98636400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr9:98627200-98634800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr9:98628000-98636400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr9:98628200-98636200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr9:98628400-98636800	Weak transcription	Thymus	Thymus
17	chr9:98629200-98636600	Weak transcription	Primary B cells from cord blood	blood
18	chr9:98630000-98634200	Weak transcription	HSMM	muscle
19	chr9:98630200-98634200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr9:98630200-98636200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr9:98630400-98636600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr9:98630600-98636200	Weak transcription	Brain Anterior Caudate	brain
23	chr9:98630600-98636400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr9:98630800-98634600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr9:98631000-98634200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr9:98631200-98636000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr9:98631200-98636600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr9:98631200-98636600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr9:98631200-98636600	Weak transcription	NH-A	brain
30	chr9:98631400-98636400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr9:98631400-98636600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr9:98631400-98636600	Weak transcription	Osteobl	bone
33	chr9:98631800-98636400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr9:98631800-98636400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr9:98631800-98636800	Weak transcription	Ovary	ovary
36	chr9:98632000-98636800	Weak transcription	Esophagus	oesophagus
37	chr9:98632200-98636400	Weak transcription	Fetal Intestine Small	intestine
38	chr9:98632200-98636600	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr9:98632400-98634000	Enhancers	Primary hematopoietic stem cells	blood
40	chr9:98632400-98634000	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr9:98632400-98634200	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr9:98632400-98636800	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr9:98632600-98634400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr9:98632600-98634400	Weak transcription	Brain Substantia Nigra	brain
45	chr9:98632600-98636000	Weak transcription	Brain Hippocampus Middle	brain
46	chr9:98632600-98636600	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr9:98632800-98634800	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr9:98632800-98635400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr9:98632800-98636400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr9:98632800-98636800	Weak transcription	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links