Variant report

Variant	rs16911713
Chromosome Location	chr9:97571249-97571250
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:97563933..97571351-chr9:97576672..97582632,18	MCF-7	breast:
2	chr9:97565914..97571490-chr9:97674207..97687450,22	MCF-7	breast:
3	chr9:97568707..97571260-chr9:97810140..97811755,2	MCF-7	breast:
4	chr9:97562492..97588737-chr9:97670126..97691056,102	MCF-7	breast:
5	chr9:97569515..97571628-chr9:97628537..97630487,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000148120	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10122127	1.00[JPT][hapmap]
rs1028843	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10512234	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[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10512236	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[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10732405	1.00[JPT][hapmap];0.83[MKK][hapmap]
rs10993325	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10993329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10993337	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10993340	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10993341	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10993349	1.00[CEU][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10993350	0.81[EUR][1000 genomes]
rs10993351	1.00[JPT][hapmap]
rs10993360	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10993362	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10993363	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10993364	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10993381	0.93[GIH][hapmap];1.00[TSI][hapmap]
rs10993391	1.00[TSI][hapmap]
rs12336061	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12336308	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12336437	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12337706	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12337992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12338982	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12340107	0.88[TSI][hapmap]
rs12341764	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12341814	1.00[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];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12343530	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[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12344052	0.93[GIH][hapmap];1.00[TSI][hapmap]
rs12344157	1.00[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];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12344256	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12345098	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12345321	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12345763	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12345783	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12346548	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12347744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12348060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12348206	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12351111	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12352600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12352856	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16911670	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2025793	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2165715	0.83[MKK][hapmap]
rs2304884	1.00[JPT][hapmap]
rs242259	1.00[JPT][hapmap]
rs34335636	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs356135	1.00[JPT][hapmap];0.83[MKK][hapmap]
rs376902	1.00[JPT][hapmap];0.83[MKK][hapmap]
rs3808890	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3858088	1.00[JPT][hapmap]
rs41281168	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4744380	1.00[JPT][hapmap];0.83[MKK][hapmap]
rs60048957	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60514919	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61446634	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6479566	1.00[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap]
rs7031172	1.00[JPT][hapmap]
rs7045387	1.00[JPT][hapmap]
rs7866487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7869666	1.00[JPT][hapmap]
rs925813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9987493	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9987549	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9987803	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[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	nsv893596	chr9:97321172-97598966	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16911713	C9orf3	cis	lymphoblastoid	seeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:97556800-97575800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr9:97562000-97572800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr9:97563400-97584200	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr9:97563600-97594400	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr9:97563800-97573400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr9:97563800-97573800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr9:97563800-97574600	Weak transcription	Colon Smooth Muscle	Colon
8	chr9:97563800-97579600	Weak transcription	Gastric	stomach
9	chr9:97563800-97584200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr9:97564000-97574400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr9:97564000-97574400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr9:97564000-97574600	Weak transcription	Stomach Smooth Muscle	stomach
13	chr9:97564000-97580000	Weak transcription	Primary B cells from peripheral blood	blood
14	chr9:97564000-97589200	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr9:97564200-97580400	Weak transcription	K562	blood
16	chr9:97565200-97572200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr9:97565200-97587000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr9:97565400-97572200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr9:97565400-97572200	Weak transcription	Esophagus	oesophagus
20	chr9:97565400-97584200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr9:97567200-97571400	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr9:97567200-97571400	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr9:97567400-97593400	Weak transcription	Thymus	Thymus
24	chr9:97567600-97572200	Weak transcription	Spleen	Spleen
25	chr9:97567600-97579400	Weak transcription	Pancreas	Pancrea
26	chr9:97568000-97571600	Enhancers	Fetal Heart	heart
27	chr9:97568200-97571400	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr9:97568200-97575800	Weak transcription	Rectal Smooth Muscle	rectum
29	chr9:97568600-97581400	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr9:97568600-97589000	Weak transcription	Liver	Liver
31	chr9:97568800-97573800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr9:97568800-97574400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr9:97568800-97581400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr9:97568800-97581400	Weak transcription	Fetal Brain Male	brain
35	chr9:97568800-97586800	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr9:97569000-97572400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr9:97569000-97574400	Weak transcription	NHLF	lung
38	chr9:97569000-97575400	Weak transcription	Fetal Brain Female	brain
39	chr9:97569000-97580200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr9:97569000-97583800	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr9:97569000-97584200	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr9:97569000-97584200	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr9:97569200-97571400	Enhancers	Aorta	Aorta
44	chr9:97569200-97571800	Strong transcription	Primary B cells from cord blood	blood
45	chr9:97569200-97572200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr9:97569200-97572400	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr9:97569200-97572600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr9:97569200-97574200	Strong transcription	Fetal Intestine Large	intestine
49	chr9:97569200-97574400	Strong transcription	Primary T cells from cord blood	blood
50	chr9:97569200-97581200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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