Variant report

Variant	rs9399697
Chromosome Location	chr6:101322202-101322203
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:101316563..101319212-chr6:101321882..101324252,3	K562	blood:
2	chr6:101319726..101322538-chr6:101323434..101327261,5	K562	blood:
3	chr6:101184266..101186701-chr6:101321079..101322607,2	K562	blood:
4	chr6:101321078..101323999-chr6:101327365..101330497,3	K562	blood:
5	chr6:101321574..101324468-chr6:101327088..101328680,2	MCF-7	breast:
6	chr6:101315511..101317723-chr6:101321403..101323944,2	K562	blood:

Variant related genes	Relation type
ENSG00000112249	Chromatin interaction
ENSG00000260000	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11155708	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11755579	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11758174	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12209186	0.91[ASN][1000 genomes]
rs13193416	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13205402	0.80[EUR][1000 genomes]
rs13212730	0.81[EUR][1000 genomes]
rs13220881	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17672397	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1813223	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2004276	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2398247	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34555037	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34716527	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4840157	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4840160	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4840164	0.80[EUR][1000 genomes]
rs62420689	0.81[EUR][1000 genomes]
rs62422111	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6917195	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9322270	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9322271	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9322276	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9322279	0.83[AMR][1000 genomes]
rs9377236	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9377240	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9377241	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9386258	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9390698	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9390702	0.83[AMR][1000 genomes]
rs9399695	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9404059	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9404060	0.83[ASN][1000 genomes]
rs979122	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9791225	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949535	chr6:100740293-101469052	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1020692	chr6:101136992-101426071	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv886457	chr6:101158950-101487473	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
4	nsv1020400	chr6:101172705-101981665	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv538390	chr6:101172705-101981665	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv1019213	chr6:101225650-101623140	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv538391	chr6:101225650-101623140	Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	esv2763587	chr6:101277874-101510491	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9399697	ASCC3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:101269200-101326600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:101285600-101326600	Weak transcription	NHLF	lung
3	chr6:101291200-101326400	Weak transcription	Brain Anterior Caudate	brain
4	chr6:101294600-101325400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr6:101294600-101328600	Weak transcription	Spleen	Spleen
6	chr6:101294800-101325600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr6:101295000-101325800	Weak transcription	Brain Angular Gyrus	brain
8	chr6:101295000-101325800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr6:101296000-101323400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr6:101296800-101323800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr6:101297000-101327200	Weak transcription	Fetal Muscle Leg	muscle
12	chr6:101297000-101328200	Weak transcription	Ovary	ovary
13	chr6:101300200-101326600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr6:101300200-101328400	Weak transcription	Esophagus	oesophagus
15	chr6:101300200-101328400	Weak transcription	Lung	lung
16	chr6:101302600-101327800	Weak transcription	Stomach Mucosa	stomach
17	chr6:101303800-101325600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr6:101304200-101326600	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr6:101304400-101327800	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr6:101304800-101325400	Weak transcription	Brain Substantia Nigra	brain
21	chr6:101305000-101327800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr6:101309800-101326600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr6:101311200-101323400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr6:101311600-101326400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr6:101311600-101327800	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr6:101311800-101326400	Weak transcription	Duodenum Mucosa	Duodenum
27	chr6:101311800-101326600	Weak transcription	Pancreas	Pancrea
28	chr6:101311800-101326600	Weak transcription	Thymus	Thymus
29	chr6:101311800-101328200	Weak transcription	Aorta	Aorta
30	chr6:101311800-101328400	Weak transcription	Fetal Muscle Trunk	muscle
31	chr6:101311800-101328400	Weak transcription	Left Ventricle	heart
32	chr6:101313000-101327200	Weak transcription	Fetal Intestine Large	intestine
33	chr6:101314800-101326400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr6:101314800-101326800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr6:101315000-101325600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr6:101315200-101327800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr6:101315600-101327200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr6:101315800-101323400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr6:101315800-101325600	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr6:101315800-101325800	Weak transcription	NHEK	skin
41	chr6:101315800-101326400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr6:101315800-101327200	Weak transcription	Adipose Nuclei	Adipose
43	chr6:101315800-101327200	Weak transcription	Placenta	Placenta
44	chr6:101315800-101327800	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr6:101316000-101323400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr6:101316000-101323400	Weak transcription	Liver	Liver
47	chr6:101316000-101324200	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr6:101316000-101325000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr6:101316000-101325600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr6:101316000-101325600	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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