Variant report

Variant	rs9498383
Chromosome Location	chr6:149934177-149934178
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:149927260..149929219-chr6:149933364..149935307,2	MCF-7	breast:
2	chr16:84500130..84500905-chr6:149934076..149935073,3	MCF-7	breast:

Extended variants
information (count: 97 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10747275	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10782310	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10782311	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10782312	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10782313	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1080670	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11155662	0.82[ASN][1000 genomes]
rs11155668	0.83[ASN][1000 genomes]
rs11155669	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11155670	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs11155671	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12174716	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12183664	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12191643	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12193364	0.84[AMR][1000 genomes]
rs12206402	0.83[ASN][1000 genomes]
rs12523793	0.81[ASN][1000 genomes]
rs12529698	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12662174	0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2064520	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2064521	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs34157004	0.81[AMR][1000 genomes]
rs35961297	0.81[AMR][1000 genomes]
rs3734295	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3777949	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3924871	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4869812	0.82[AMR][1000 genomes]
rs4870144	0.84[AMR][1000 genomes]
rs4870267	0.82[AMR][1000 genomes]
rs55849538	0.85[ASN][1000 genomes]
rs55993747	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs56091542	0.85[ASN][1000 genomes]
rs57938011	0.83[ASN][1000 genomes]
rs62439811	0.83[ASN][1000 genomes]
rs62439836	0.82[AMR][1000 genomes]
rs7381555	0.82[AMR][1000 genomes]
rs7740278	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9285522	0.81[ASN][1000 genomes]
rs9285523	0.83[AMR][1000 genomes]
rs9322188	0.82[ASN][1000 genomes]
rs9322189	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9322194	0.82[ASN][1000 genomes]
rs9322196	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9322197	0.82[ASN][1000 genomes]
rs9322198	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9322199	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9322200	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9322204	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9322207	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9322208	0.85[AMR][1000 genomes]
rs9377228	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9377229	0.81[ASN][1000 genomes]
rs9377230	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9379314	0.86[AMR][1000 genomes]
rs9379348	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9393132	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9399692	0.84[AMR][1000 genomes]
rs9399693	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9404047	0.84[ASN][1000 genomes]
rs9404048	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9406286	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9406346	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9485405	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9485408	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9498382	0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9498384	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9505823	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9505824	0.84[AMR][1000 genomes]
rs9505982	0.81[ASN][1000 genomes]
rs9688452	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9688794	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9688858	0.82[ASN][1000 genomes]
rs9688861	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9689084	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9689599	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9689716	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9689723	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9718079	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9766037	0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9766886	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9767105	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9767123	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9767554	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9767555	0.81[ASN][1000 genomes]
rs9767713	0.82[ASN][1000 genomes]
rs9800580	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9800603	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9800614	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9800686	0.80[ASN][1000 genomes]
rs9800736	0.81[ASN][1000 genomes]
rs9800871	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9968911	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv289	chr6:149864898-149998818	Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv5534	chr6:149864898-149998818	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv886762	chr6:149866452-150174507	Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	esv1794633	chr6:149903597-149944908	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv1792620	chr6:149909491-150083621	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs9498383	NUP43	cis	Whole Blood	GTEx
rs9498383	GINM1	cis	Whole Blood	GTEx
rs9498383	RP11-350J20.5	cis	lung	GTEx
rs9498383	RP11-350J20.5	cis	Esophagus Muscularis	GTEx
rs9498383	NUP43	Cis_1M	lymphoblastoid	RTeQTL
rs9498383	RP11-350J20.5	cis	Esophagus Mucosa	GTEx
rs9498383	RP11-350J20.5	cis	Skin Sun Exposed Lower leg	GTEx
rs9498383	RP11-350J20.5	cis	Thyroid	GTEx
rs9498383	C6orf72	Cis_1M	lymphoblastoid	RTeQTL
rs9498383	RP11-350J20.5	cis	Artery Aorta	GTEx
rs9498383	RP11-350J20.9	cis	Esophagus Mucosa	GTEx
rs9498383	RP11-350J20.5	cis	Adipose Subcutaneous	GTEx
rs9498383	RP11-350J20.5	cis	Artery Tibial	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149909000-149935000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:149910000-149935200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr6:149915200-149935000	Weak transcription	Small Intestine	intestine
4	chr6:149915600-149935200	Weak transcription	Esophagus	oesophagus
5	chr6:149915600-149968400	Weak transcription	Pancreas	Pancrea
6	chr6:149915600-149969200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:149915800-149934800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr6:149915800-149969200	Weak transcription	Gastric	stomach
9	chr6:149916000-149935000	Weak transcription	Spleen	Spleen
10	chr6:149916000-149943000	Weak transcription	Colonic Mucosa	Colon
11	chr6:149916400-149934600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr6:149916400-149950200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr6:149917600-149934800	Weak transcription	Psoas Muscle	Psoas
14	chr6:149918400-149935400	Weak transcription	HMEC	breast
15	chr6:149918400-149950200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr6:149918800-149934800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr6:149918800-149934800	Weak transcription	Brain Substantia Nigra	brain
18	chr6:149918800-149967600	Weak transcription	HUVEC	blood vessel
19	chr6:149918800-149967600	Weak transcription	NHLF	lung
20	chr6:149919000-149943000	Weak transcription	NHDF-Ad	bronchial
21	chr6:149919200-149935000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr6:149919400-149934800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr6:149919400-149940600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr6:149919400-149949000	Weak transcription	Osteobl	bone
25	chr6:149919600-149935000	Weak transcription	Lung	lung
26	chr6:149919800-149934400	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr6:149919800-149934800	Weak transcription	Ovary	ovary
28	chr6:149919800-149935000	Weak transcription	Aorta	Aorta
29	chr6:149920400-149940200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr6:149920600-149934400	Weak transcription	K562	blood
31	chr6:149920800-149935000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr6:149920800-149935000	Weak transcription	Left Ventricle	heart
33	chr6:149921000-149944000	Weak transcription	HSMMtube	muscle
34	chr6:149921400-149934600	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr6:149922000-149934800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr6:149922800-149934400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr6:149923000-149934400	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr6:149923000-149935000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr6:149923000-149941000	Weak transcription	HSMM	muscle
40	chr6:149923000-149943000	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr6:149923000-149952200	Weak transcription	NH-A	brain
42	chr6:149923200-149942800	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr6:149923400-149935000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr6:149923400-149947600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr6:149923800-149934600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr6:149924800-149934400	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr6:149924800-149934600	Weak transcription	Fetal Brain Female	brain
48	chr6:149924800-149934800	Weak transcription	Brain Angular Gyrus	brain
49	chr6:149924800-149934800	Weak transcription	Fetal Heart	heart
50	chr6:149924800-149941000	Weak transcription	Rectal Smooth Muscle	rectum

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