Variant report

Variant	rs356677
Chromosome Location	chr9:98000572-98000573
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1045276	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap]
rs10491560	1.00[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap]
rs171417	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs184818	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs187172	1.00[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes]
rs2282216	0.85[JPT][hapmap]
rs356666	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.96[MKK][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs356669	0.81[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes]
rs356673	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs356675	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs356678	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs356679	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs356680	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs356682	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs356683	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs356684	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs356687	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs356688	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs356689	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3780567	0.90[JPT][hapmap]
rs3824486	0.85[JPT][hapmap]
rs416792	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs437511	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4647376	0.95[JPT][hapmap];0.82[TSI][hapmap]
rs4647534	0.90[JPT][hapmap]
rs4744451	0.90[JPT][hapmap]
rs526189	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs540412	0.91[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs565293	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs609324	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs657637	1.00[CEU][hapmap];0.81[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7033633	1.00[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs944934	0.91[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831657	chr9:97959274-98204769	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs356677	SYK	cis	parietal	SCAN
rs356677	NINJ1	cis	cerebellum	SCAN
rs356677	TDRD7	cis	cerebellum	SCAN
rs356677	PHF2	cis	cerebellum	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97973600-98024000	Weak transcription	Gastric	stomach
2	chr9:97974000-98009400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr9:97978000-98008400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr9:97981400-98012400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr9:97981600-98009000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr9:97983400-98012400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr9:97987200-98015400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr9:97987800-98008400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr9:97988200-98007200	Weak transcription	Fetal Lung	lung
10	chr9:97988400-98012200	Weak transcription	Fetal Kidney	kidney
11	chr9:97989200-98009600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr9:97989200-98012400	Weak transcription	Ovary	ovary
13	chr9:97989400-98012400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr9:97989400-98013400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr9:97989600-98006400	Weak transcription	Fetal Muscle Trunk	muscle
16	chr9:97989600-98012200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr9:97989800-98007400	Weak transcription	Duodenum Mucosa	Duodenum
18	chr9:97989800-98011200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr9:97990200-98013400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr9:97990400-98008200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr9:97990400-98012600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr9:97990800-98001200	Weak transcription	Pancreas	Pancrea
23	chr9:97991000-98010400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr9:97991200-98024000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr9:97992200-98003800	Weak transcription	NHLF	lung
26	chr9:97992200-98004600	Weak transcription	HepG2	liver
27	chr9:97992400-98008800	Weak transcription	Right Ventricle	heart
28	chr9:97992600-98002200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr9:97992600-98013400	Weak transcription	Liver	Liver
30	chr9:97993000-98008400	Weak transcription	Adipose Nuclei	Adipose
31	chr9:97993200-98008400	Weak transcription	Spleen	Spleen
32	chr9:97993800-98008800	Weak transcription	Lung	lung
33	chr9:97994000-98006200	Weak transcription	Fetal Muscle Leg	muscle
34	chr9:97994200-98001200	Weak transcription	Fetal Stomach	stomach
35	chr9:97994200-98011400	Weak transcription	Hela-S3	cervix
36	chr9:97994600-98002200	Weak transcription	Esophagus	oesophagus
37	chr9:97994600-98006200	Weak transcription	Fetal Intestine Large	intestine
38	chr9:97994600-98008200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr9:97994600-98008400	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr9:97994800-98002000	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr9:97994800-98008000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr9:97994800-98011200	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr9:97994800-98017200	Weak transcription	Primary hematopoietic stem cells	blood
44	chr9:97995200-98008200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr9:97995200-98008200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr9:97995400-98012800	Weak transcription	HSMM	muscle
47	chr9:97996000-98001800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr9:97996400-98002200	Weak transcription	Left Ventricle	heart
49	chr9:97996400-98012400	Weak transcription	Psoas Muscle	Psoas
50	chr9:97996600-98004000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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