Variant report

Variant	rs4742781
Chromosome Location	chr9:98645674-98645675
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:98644374..98646998-chr9:98660119..98662324,2	MCF-7	breast:
2	chr9:98643243..98646230-chr9:98646548..98650436,4	MCF-7	breast:
3	chr9:98642876..98646721-chr9:98647995..98651810,4	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10983321	0.85[CEU][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10988581	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10988792	0.81[ASW][hapmap];0.86[LWK][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap]
rs10988804	0.89[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11787559	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11790370	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11790491	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11793298	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11794054	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12001	0.92[GIH][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs12683310	0.82[EUR][1000 genomes]
rs12683634	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12685221	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12685807	0.92[GIH][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs12686222	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12686457	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1360064	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16910262	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16910296	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16910298	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16910418	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1831228	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1999023	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2026032	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2069053	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2274654	0.81[ASW][hapmap];0.89[GIH][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap]
rs34533243	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3780574	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4532708	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4742775	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4743372	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]
rs4743391	0.82[EUR][1000 genomes]
rs4743417	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs4743418	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4743436	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4743472	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7048414	0.90[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73536517	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73656544	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7868270	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4742781	C9orf130	Cis_1M	lymphoblastoid	RTeQTL
rs4742781	LINC00476	cis	Whole Blood	GTEx
rs4742781	LINC00476	cis	Esophagus Mucosa	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98638800-98648000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:98638800-98648400	Weak transcription	Lung	lung
3	chr9:98638800-98649000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr9:98638800-98654800	Weak transcription	Esophagus	oesophagus
5	chr9:98638800-98702200	Weak transcription	Pancreas	Pancrea
6	chr9:98639400-98647800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr9:98639400-98649000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr9:98639400-98650800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr9:98639400-98677800	Weak transcription	Placenta	Placenta
10	chr9:98639400-98678000	Weak transcription	Ovary	ovary
11	chr9:98639600-98646200	Weak transcription	HSMMtube	muscle
12	chr9:98639600-98649200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr9:98639600-98678000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr9:98639800-98664200	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr9:98639800-98677800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr9:98640000-98649000	Weak transcription	Spleen	Spleen
17	chr9:98640000-98661600	Weak transcription	Right Atrium	heart
18	chr9:98640000-98663600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr9:98640000-98678200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr9:98640000-98680600	Weak transcription	Colonic Mucosa	Colon
21	chr9:98640000-98685600	Weak transcription	Right Ventricle	heart
22	chr9:98640000-98718600	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr9:98640200-98678200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr9:98640400-98649200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr9:98640400-98664800	Weak transcription	Brain Substantia Nigra	brain
26	chr9:98640400-98677800	Weak transcription	Psoas Muscle	Psoas
27	chr9:98640600-98647800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr9:98640600-98649000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr9:98640600-98678000	Weak transcription	Brain Cingulate Gyrus	brain
30	chr9:98641400-98646400	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr9:98641600-98650000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr9:98642000-98647200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr9:98642000-98647600	Weak transcription	Fetal Brain Male	brain
34	chr9:98642200-98647600	Weak transcription	Fetal Heart	heart
35	chr9:98642200-98652400	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr9:98642200-98654600	Weak transcription	Fetal Intestine Small	intestine
37	chr9:98642200-98663600	Weak transcription	Hela-S3	cervix
38	chr9:98642600-98678000	Weak transcription	Colon Smooth Muscle	Colon
39	chr9:98642600-98680600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr9:98642800-98668200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr9:98642800-98681800	Weak transcription	Fetal Kidney	kidney
42	chr9:98643000-98645800	Weak transcription	NH-A	brain
43	chr9:98643000-98648400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr9:98643200-98645800	Strong transcription	Primary B cells from peripheral blood	blood
45	chr9:98643200-98647800	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr9:98643200-98648200	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr9:98643200-98648400	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr9:98643200-98649000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr9:98643200-98649800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr9:98643200-98651200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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