Variant report

Variant	rs356660
Chromosome Location	chr9:98006135-98006136
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	chr9:98003959..98008531-chr9:98008535..98011761,4	K562	blood:
2	chr9:98005780..98007562-chr9:98010261..98012480,2	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10761371	1.00[JPT][hapmap]
rs10993471	1.00[JPT][hapmap]
rs1564235	1.00[JPT][hapmap]
rs1623009	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs173339	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1871220	1.00[JPT][hapmap]
rs1888944	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs242448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2655055	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2765817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs356661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs356662	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs356663	0.86[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];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs356671	0.86[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];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs356685	0.86[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];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs356686	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3780560	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs400727	1.00[CEU][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs420089	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4647379	1.00[MKK][hapmap];0.80[YRI][hapmap]
rs4647513	1.00[MKK][hapmap];1.00[YRI][hapmap]
rs4647551	1.00[LWK][hapmap];1.00[MKK][hapmap];0.83[YRI][hapmap]
rs4743989	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4744437	0.91[CEU][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap]
rs4744440	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs475413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs607105	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs648615	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs651009	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.83[TSI][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7033294	1.00[YRI][hapmap]
rs7038007	0.86[AFR][1000 genomes]
rs7049188	0.90[YRI][hapmap]
rs7866396	0.82[YRI][hapmap]
rs9299427	0.94[AMR][1000 genomes];0.89[EUR][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
rs356660	TPM2	trans	lymphoblastoid	seeQTL
rs356660	GJB2	trans	brain	seeQTL
rs356660	MIR23B	cis	lymphoblastoid	seeQTL
rs356660	CYP1B1	trans	brain	seeQTL

Chromatin state (count:69 , 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	chr9:97991000-98010400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr9:97991200-98024000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr9:97992400-98008800	Weak transcription	Right Ventricle	heart
25	chr9:97992600-98013400	Weak transcription	Liver	Liver
26	chr9:97993000-98008400	Weak transcription	Adipose Nuclei	Adipose
27	chr9:97993200-98008400	Weak transcription	Spleen	Spleen
28	chr9:97993800-98008800	Weak transcription	Lung	lung
29	chr9:97994000-98006200	Weak transcription	Fetal Muscle Leg	muscle
30	chr9:97994200-98011400	Weak transcription	Hela-S3	cervix
31	chr9:97994600-98006200	Weak transcription	Fetal Intestine Large	intestine
32	chr9:97994600-98008200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr9:97994600-98008400	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr9:97994800-98008000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr9:97994800-98011200	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr9:97994800-98017200	Weak transcription	Primary hematopoietic stem cells	blood
37	chr9:97995200-98008200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr9:97995200-98008200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr9:97995400-98012800	Weak transcription	HSMM	muscle
40	chr9:97996400-98012400	Weak transcription	Psoas Muscle	Psoas
41	chr9:97996800-98012800	Weak transcription	HSMMtube	muscle
42	chr9:97997400-98009000	Weak transcription	GM12878-XiMat	blood
43	chr9:97997600-98012400	Weak transcription	Fetal Brain Male	brain
44	chr9:97997800-98007200	Weak transcription	Primary T cells from cord blood	blood
45	chr9:97999800-98019000	Weak transcription	Aorta	Aorta
46	chr9:98000800-98008200	Weak transcription	Thymus	Thymus
47	chr9:98001200-98012400	Weak transcription	Rectal Smooth Muscle	rectum
48	chr9:98002000-98007200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr9:98002200-98008800	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr9:98002400-98008800	Weak transcription	Rectal Mucosa Donor 29	rectum

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