Variant report

Variant	rs17813663
Chromosome Location	chr9:103208131-103208132
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:103207631..103208140-chr9:103357331..103358167,2	MCF-7	breast:
2	chr9:103188632..103190221-chr9:103206749..103208977,2	MCF-7	breast:
3	chr9:103206264..103208362-chr9:103209837..103212549,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000066697	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1016176	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1016177	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10819788	0.80[MEX][hapmap]
rs10989090	0.81[EUR][1000 genomes]
rs10989092	0.81[EUR][1000 genomes]
rs10989127	0.80[MEX][hapmap]
rs12004257	0.80[MEX][hapmap]
rs12237166	0.82[EUR][1000 genomes]
rs1332598	0.80[MEX][hapmap]
rs17740576	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MKK][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17741842	0.84[ASW][hapmap];0.95[GIH][hapmap];0.93[MEX][hapmap]
rs17813447	1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17813801	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17813854	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17814768	0.81[CEU][hapmap];0.90[GIH][hapmap];0.93[MEX][hapmap]
rs17814828	0.95[GIH][hapmap];0.86[MEX][hapmap]
rs1930238	0.93[MEX][hapmap]
rs2026998	1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2151107	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2274882	0.80[MEX][hapmap]
rs35438121	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41274963	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4395949	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.92[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56179916	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56313595	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56720423	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57241635	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58030694	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58698990	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59668196	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61306839	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61386923	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7034154	0.80[EUR][1000 genomes]
rs7041189	0.95[GIH][hapmap];0.93[MEX][hapmap]
rs7041933	0.80[EUR][1000 genomes]
rs7046659	0.87[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs72733393	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72733395	0.86[EUR][1000 genomes]
rs72733397	0.85[EUR][1000 genomes]
rs72735110	0.80[EUR][1000 genomes]
rs73655529	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73655530	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73655531	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73655532	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73655533	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73655534	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73655535	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73655536	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73655537	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73655539	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655540	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655541	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655542	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655543	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655544	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655545	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655546	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655547	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73655549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73655550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73655551	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73655553	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73655554	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7865385	0.95[GIH][hapmap];0.93[MEX][hapmap]

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	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv825012	chr9:103152205-103256281	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv614955	chr9:103181596-103261227	ZNF genes & repeats Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17813663	C9orf30	cis	lymphoblastoid	seeQTL
rs17813663	LOC286359	cis	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103190400-103214200	Weak transcription	Thymus	Thymus
2	chr9:103190600-103214400	Weak transcription	Primary B cells from cord blood	blood
3	chr9:103190600-103224600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr9:103190800-103213200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr9:103190800-103217600	Weak transcription	Fetal Intestine Large	intestine
6	chr9:103191200-103214200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr9:103191600-103209200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr9:103191600-103209200	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr9:103191600-103212800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr9:103191600-103213000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr9:103191600-103214400	Weak transcription	Esophagus	oesophagus
12	chr9:103191800-103217600	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr9:103191800-103228000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr9:103192000-103214000	Weak transcription	Colon Smooth Muscle	Colon
15	chr9:103192200-103210600	Weak transcription	Stomach Smooth Muscle	stomach
16	chr9:103192600-103213200	Weak transcription	Fetal Brain Male	brain
17	chr9:103193000-103214400	Weak transcription	Pancreas	Pancrea
18	chr9:103194600-103213200	Weak transcription	Lung	lung
19	chr9:103196200-103226400	Weak transcription	Psoas Muscle	Psoas
20	chr9:103197200-103211600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr9:103198400-103210400	Weak transcription	GM12878-XiMat	blood
22	chr9:103199800-103208400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr9:103200000-103217000	Weak transcription	K562	blood
24	chr9:103201000-103208200	Weak transcription	Brain Hippocampus Middle	brain
25	chr9:103201200-103215600	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr9:103201600-103215400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr9:103202000-103213400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr9:103202000-103215800	Weak transcription	Fetal Thymus	thymus
29	chr9:103202600-103213800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr9:103202800-103208200	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr9:103202800-103217400	Weak transcription	Right Ventricle	heart
32	chr9:103203800-103215600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr9:103203800-103217400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr9:103204000-103214000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr9:103204000-103216800	Strong transcription	Osteobl	bone
36	chr9:103204200-103211000	Strong transcription	NH-A	brain
37	chr9:103204200-103214000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr9:103204400-103209400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr9:103204400-103212600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr9:103204600-103221200	Weak transcription	Fetal Kidney	kidney
41	chr9:103204800-103212800	Weak transcription	Adipose Nuclei	Adipose
42	chr9:103204800-103213200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr9:103204800-103213200	Weak transcription	Placenta	Placenta
44	chr9:103205000-103208800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr9:103205000-103213000	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr9:103205000-103213600	Weak transcription	Primary B cells from peripheral blood	blood
47	chr9:103205000-103214200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr9:103205000-103214400	Weak transcription	Gastric	stomach
49	chr9:103205000-103216800	Weak transcription	Fetal Intestine Small	intestine
50	chr9:103206000-103208600	Enhancers	Fetal Heart	heart

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