Variant report

Variant	rs9399696
Chromosome Location	chr6:101295873-101295874
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:101294725..101296598-chr6:101316147..101318633,2	K562	blood:
2	chr6:101271307..101273305-chr6:101294411..101297319,2	K562	blood:
3	chr6:101286243..101289209-chr6:101295205..101297234,2	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs12527901	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12664068	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1854483	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3734351	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4098482	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56115902	0.93[ASN][1000 genomes]
rs57454377	0.87[ASN][1000 genomes]
rs57795969	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61289570	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6916271	0.91[AFR][1000 genomes]
rs6927027	0.94[GIH][hapmap]
rs6930051	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72610823	0.98[ASN][1000 genomes]
rs72610824	0.82[ASN][1000 genomes]
rs7748160	0.83[ASN][1000 genomes]
rs9377233	0.90[CHB][hapmap]
rs9377246	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9377247	0.85[ASN][1000 genomes]
rs9386259	0.84[ASW][hapmap];0.90[LWK][hapmap];0.86[MKK][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs9386260	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9386262	0.81[ASN][1000 genomes]
rs9390697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9390699	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9390700	0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9404055	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9404058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9404063	0.85[ASN][1000 genomes]
rs9485415	0.87[CEU][hapmap];0.81[CHB][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9498392	0.90[CHB][hapmap]
rs9498408	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9498409	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9498411	0.86[AFR][1000 genomes]
rs9498414	0.92[ASW][hapmap];1.00[CEU][hapmap];0.90[LWK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9498418	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9498439	0.87[CEU][hapmap];0.85[CHB][hapmap];0.89[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9791284	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv1016353	chr6:101172705-101304041	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9399696	ASCC3	cis	Nerve Tibial	GTEx
rs9399696	GRIK2	cis	Artery Tibial	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:101184400-101304600	Weak transcription	Hela-S3	cervix
2	chr6:101215200-101311400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr6:101233600-101306600	Weak transcription	K562	blood
4	chr6:101238000-101296200	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr6:101244600-101296200	Weak transcription	NH-A	brain
6	chr6:101249400-101298200	Weak transcription	A549	lung
7	chr6:101253400-101304200	Weak transcription	Primary T cells from cord blood	blood
8	chr6:101269200-101326600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr6:101271200-101296000	Weak transcription	Ovary	ovary
10	chr6:101271400-101296000	Weak transcription	HSMMtube	muscle
11	chr6:101275800-101314400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr6:101277400-101299800	Weak transcription	Esophagus	oesophagus
13	chr6:101277600-101296000	Weak transcription	Fetal Intestine Large	intestine
14	chr6:101277600-101296400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr6:101277600-101296400	Weak transcription	Fetal Muscle Leg	muscle
16	chr6:101277600-101299600	Weak transcription	Thymus	Thymus
17	chr6:101277600-101299800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr6:101278000-101306600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr6:101278000-101313800	Weak transcription	Fetal Intestine Small	intestine
20	chr6:101278600-101296000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr6:101279400-101298200	Weak transcription	NHEK	skin
22	chr6:101281200-101317000	Weak transcription	Small Intestine	intestine
23	chr6:101281800-101299600	Weak transcription	Fetal Stomach	stomach
24	chr6:101282000-101296200	Weak transcription	Left Ventricle	heart
25	chr6:101282000-101311400	Weak transcription	Aorta	Aorta
26	chr6:101283000-101301600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr6:101284800-101304000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr6:101285000-101304400	Weak transcription	Brain Substantia Nigra	brain
29	chr6:101285600-101326600	Weak transcription	NHLF	lung
30	chr6:101287800-101313000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr6:101289200-101304800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr6:101289400-101302600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:101289800-101304400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr6:101290200-101304200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr6:101290200-101306600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr6:101290200-101318200	Weak transcription	Fetal Lung	lung
37	chr6:101290600-101312800	Weak transcription	Fetal Brain Male	brain
38	chr6:101290800-101296200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr6:101290800-101311400	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr6:101290800-101311600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr6:101291200-101326400	Weak transcription	Brain Anterior Caudate	brain
42	chr6:101291400-101314000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr6:101291600-101314000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr6:101291800-101312800	Weak transcription	Gastric	stomach
45	chr6:101292600-101310800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr6:101293200-101296200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr6:101293200-101299800	Weak transcription	Lung	lung
48	chr6:101293600-101298400	Weak transcription	Psoas Muscle	Psoas
49	chr6:101294000-101297000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr6:101294000-101320400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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