Variant report

Variant	rs4743372
Chromosome Location	chr9:98630743-98630744
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:98562023..98564379-chr9:98630316..98632934,2	MCF-7	breast:
2	chr9:98614433..98624477-chr9:98629889..98639636,23	MCF-7	breast:
3	chr9:98623383..98625776-chr9:98629307..98631395,2	MCF-7	breast:
4	chr9:98629164..98632859-chr9:98633356..98639163,9	K562	blood:
5	chr9:98626986..98632585-chr9:98632790..98639988,21	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PTCH1-8	chr9:98630174-98630835	NONHSAT133400

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

Extended variants
information (count: 40 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10759883	0.96[YRI][hapmap]
rs10983321	1.00[CEU][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10988581	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10988804	0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11787559	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11790370	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11790491	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11793298	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11794054	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12001	1.00[YRI][hapmap];0.99[AFR][1000 genomes]
rs12683634	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12685221	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12685807	1.00[YRI][hapmap];0.99[AFR][1000 genomes]
rs12686222	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12686457	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1360064	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16910262	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16910296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16910298	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];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16910418	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1831228	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1999023	0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2026032	0.82[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2069053	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34533243	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3780574	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4532708	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4742775	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4742781	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4743418	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4743436	0.91[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4743472	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7048414	1.00[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73536517	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73656544	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7868270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4743372	C9orf130	cis	multi-tissue	Pritchard
rs4743372	NA	cis	multi-tissue	Pritchard
rs4743372	LINC00476	cis	Whole Blood	GTEx
rs4743372	LINC00476	cis	Skin Sun Exposed Lower leg	GTEx
rs4743372	LINC00476	cis	Esophagus Mucosa	GTEx
rs4743372	C9orf130	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:32 , 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	chr9:98627000-98631800	Weak transcription	Fetal Intestine Small	intestine
20	chr9:98627200-98634800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr9:98628000-98636400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr9:98628200-98636200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr9:98628400-98636800	Weak transcription	Thymus	Thymus
24	chr9:98629200-98636600	Weak transcription	Primary B cells from cord blood	blood
25	chr9:98629400-98631600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr9:98629600-98631600	Weak transcription	Liver	Liver
27	chr9:98630000-98634200	Weak transcription	HSMM	muscle
28	chr9:98630200-98634200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr9:98630200-98636200	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr9:98630400-98636600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr9:98630600-98636200	Weak transcription	Brain Anterior Caudate	brain
32	chr9:98630600-98636400	Weak transcription	Rectal Smooth Muscle	rectum

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