Variant report

Variant	rs13296166
Chromosome Location	chr9:101812072-101812073
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:101786925..101789354-chr9:101811667..101813513,2	K562	blood:
2	chr9:101801421..101804201-chr9:101810789..101812954,3	K562	blood:
3	chr9:101797627..101800388-chr9:101810354..101812234,3	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10512262	0.87[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12001981	0.93[CEU][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];0.83[TSI][hapmap];0.84[ASN][1000 genomes]
rs12352174	0.93[CEU][hapmap];0.83[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13291453	0.82[CEU][hapmap];0.84[ASN][1000 genomes]
rs13302368	0.87[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1537505	0.93[CEU][hapmap];0.83[ASN][1000 genomes]
rs1537506	0.93[CEU][hapmap];0.81[CHD][hapmap];0.92[GIH][hapmap];0.83[TSI][hapmap];0.84[ASN][1000 genomes]
rs16918146	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16918148	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16918154	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16918163	0.93[CEU][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];0.83[TSI][hapmap];0.83[ASN][1000 genomes]
rs2067986	1.00[CEU][hapmap];0.88[CHD][hapmap];0.92[GIH][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34154744	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34382379	0.84[ASN][1000 genomes]
rs34654420	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34749011	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35413276	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4563947	0.93[CEU][hapmap];0.84[ASN][1000 genomes]
rs4631520	0.84[ASN][1000 genomes]
rs6478969	0.93[CEU][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.84[ASN][1000 genomes]
rs7019613	1.00[CEU][hapmap];0.84[ASN][1000 genomes]
rs7036916	1.00[ASW][hapmap];0.93[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71501887	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7851079	0.93[CEU][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs7854112	0.87[ASW][hapmap];0.93[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7857774	0.93[CEU][hapmap]
rs928522	1.00[CEU][hapmap];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv466442	chr9:101788522-101816399	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv614954	chr9:101788522-101816399	Strong transcription Genic enhancers Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv893618	chr9:101800106-101886071	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13296166	C9orf30	cis	parietal	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101761600-101814400	Weak transcription	Gastric	stomach
2	chr9:101782000-101819800	Weak transcription	Colonic Mucosa	Colon
3	chr9:101793800-101837600	Weak transcription	Psoas Muscle	Psoas
4	chr9:101798400-101819800	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr9:101799200-101814600	Weak transcription	Pancreas	Pancrea
6	chr9:101804000-101820000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr9:101805800-101819400	Strong transcription	Adipose Nuclei	Adipose
8	chr9:101805800-101820600	Weak transcription	Right Ventricle	heart
9	chr9:101806600-101817000	Weak transcription	Left Ventricle	heart
10	chr9:101807000-101831800	Strong transcription	Fetal Muscle Trunk	muscle
11	chr9:101807400-101814200	Weak transcription	Small Intestine	intestine
12	chr9:101807400-101819000	Strong transcription	Fetal Stomach	stomach
13	chr9:101807600-101831800	Strong transcription	Fetal Muscle Leg	muscle
14	chr9:101807800-101819800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr9:101808400-101817200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr9:101808600-101812600	Weak transcription	HSMMtube	muscle
17	chr9:101809200-101812200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr9:101809200-101821600	Weak transcription	Brain Anterior Caudate	brain
19	chr9:101809800-101815000	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr9:101810000-101813000	Strong transcription	Colon Smooth Muscle	Colon
21	chr9:101810400-101816200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr9:101810600-101814600	Strong transcription	Stomach Smooth Muscle	stomach
23	chr9:101810600-101814600	Weak transcription	Spleen	Spleen
24	chr9:101810600-101816000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr9:101810600-101817600	Weak transcription	Ovary	ovary
26	chr9:101810600-101819800	Enhancers	Primary T cells fromperipheralblood	blood
27	chr9:101810800-101813200	Weak transcription	Fetal Intestine Small	intestine
28	chr9:101810800-101813400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr9:101810800-101814600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr9:101811000-101813600	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr9:101811000-101814000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr9:101811200-101812200	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr9:101811200-101812200	Strong transcription	Rectal Smooth Muscle	rectum
34	chr9:101811200-101813600	Genic enhancers	Placenta	Placenta
35	chr9:101811200-101820000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr9:101811400-101812200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr9:101811400-101812200	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr9:101811400-101812400	Enhancers	Primary T helper cells fromperipheralblood	blood
39	chr9:101811400-101813600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr9:101811400-101814800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr9:101811400-101816400	Enhancers	K562	blood
42	chr9:101811600-101812200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr9:101811600-101814200	Enhancers	NHDF-Ad	bronchial
44	chr9:101811800-101813800	Enhancers	HSMM	muscle
45	chr9:101811800-101814800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr9:101811800-101814800	Weak transcription	Fetal Thymus	thymus
47	chr9:101812000-101812200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr9:101812000-101812200	Enhancers	Esophagus	oesophagus
49	chr9:101812000-101812400	Weak transcription	Lung	lung
50	chr9:101812000-101812800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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