Variant report

Variant	rs816676
Chromosome Location	chr9:98568965-98568966
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:98562038..98564856-chr9:98568504..98570089,2	K562	blood:
2	chr9:98540410..98542743-chr9:98568688..98571195,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PTCH1-3	chr9:98568370-98576204	NONHSAT133392
2	lnc-PTCH1-3	chr9:98568376-98570719	NONHSAT133393

Extended variants
information (count: 59 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10121403	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10481647	0.86[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10739632	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10760675	0.81[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10760692	0.81[AMR][1000 genomes]
rs10818017	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10983622	0.87[CHB][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10983692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10983739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10983773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10983818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12004422	0.85[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12375861	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12553442	0.82[ASN][1000 genomes]
rs1410783	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1928253	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2117432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2164156	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2164157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2770837	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3930253	0.85[AMR][1000 genomes]
rs4743458	0.81[AMR][1000 genomes]
rs583716	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs585223	0.86[AMR][1000 genomes]
rs591579	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs601916	0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.82[AMR][1000 genomes]
rs615866	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs626264	0.81[AMR][1000 genomes]
rs631273	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes]
rs636456	0.80[AMR][1000 genomes]
rs643815	0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6478984	0.90[EUR][1000 genomes]
rs6479036	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs676453	0.85[AMR][1000 genomes]
rs680468	0.85[AMR][1000 genomes]
rs680754	0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs683829	0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs689627	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs689749	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs689820	0.81[AMR][1000 genomes]
rs689871	0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs689979	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs690222	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs690304	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs690335	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs690455	0.85[AMR][1000 genomes]
rs690484	0.80[AMR][1000 genomes]
rs700963	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];0.97[ASN][1000 genomes]
rs7024710	0.85[AMR][1000 genomes]
rs7868559	0.86[AMR][1000 genomes]
rs7874897	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs816671	0.92[CHB][hapmap];0.92[JPT][hapmap];0.96[ASN][1000 genomes]
rs816681	0.96[ASN][1000 genomes]
rs913408	0.85[AMR][1000 genomes]
rs9409321	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9409322	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[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	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs816676	LINC00476	cis	Nerve Tibial	GTEx
rs816676	LINC00476	cis	Adipose Subcutaneous	GTEx
rs816676	LINC00476	cis	Artery Aorta	GTEx
rs816676	C9orf130	Cis_1M	lymphoblastoid	RTeQTL
rs816676	LINC00476	cis	lung	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98548400-98578400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr9:98557400-98577200	Weak transcription	Pancreas	Pancrea
3	chr9:98565000-98569400	Weak transcription	HUVEC	blood vessel
4	chr9:98567400-98570800	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr9:98568000-98571400	Enhancers	Ovary	ovary
6	chr9:98568400-98569000	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr9:98568400-98569000	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr9:98568600-98569000	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr9:98568600-98569000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr9:98568600-98569000	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr9:98568600-98569200	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr9:98568600-98569400	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr9:98568600-98569600	Enhancers	Stomach Smooth Muscle	stomach
14	chr9:98568600-98570600	Enhancers	Colon Smooth Muscle	Colon
15	chr9:98568600-98570600	Enhancers	Fetal Stomach	stomach
16	chr9:98568600-98571200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr9:98568800-98569000	Enhancers	Brain Cingulate Gyrus	brain
18	chr9:98568800-98569200	Enhancers	H1 Cell Line	embryonic stem cell
19	chr9:98568800-98569200	Enhancers	Aorta	Aorta
20	chr9:98568800-98570600	Enhancers	NHLF	lung
21	chr9:98568800-98573800	Weak transcription	Brain Substantia Nigra	brain

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