Variant report

Variant	rs16908779
Chromosome Location	chr9:95849415-95849416
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:95845711..95847268-chr9:95849129..95850918,2	MCF-7	breast:
2	chr9:95828747..95830360-chr9:95848919..95850495,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10821066	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10992622	0.85[CHD][hapmap]
rs10992623	0.82[CEU][hapmap];0.85[CHD][hapmap];0.82[TSI][hapmap]
rs10992626	0.84[CEU][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992628	0.94[ASN][1000 genomes]
rs1131773	0.91[CEU][hapmap];0.83[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12004054	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12352182	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12375973	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12378451	0.90[JPT][hapmap]
rs1970623	0.86[JPT][hapmap]
rs28468656	0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4077176	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs4077177	0.81[CEU][hapmap];0.82[CHD][hapmap]
rs4077811	0.91[CEU][hapmap];0.91[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4078501	0.86[ASN][1000 genomes]
rs4341217	0.91[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4636265	0.91[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs4743886	0.86[JPT][hapmap]
rs56000948	0.84[EUR][1000 genomes]
rs57866297	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61478314	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6479448	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6479450	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7025686	0.91[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7036869	0.85[CHD][hapmap]
rs7046192	0.91[CEU][hapmap];0.85[CHD][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs7046328	0.85[LWK][hapmap];0.81[MKK][hapmap]
rs7849306	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7859109	0.91[CEU][hapmap];0.89[CHD][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs7870697	0.84[EUR][1000 genomes]
rs7870953	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9695137	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9696341	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9696357	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.98[MKK][hapmap];0.86[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526296	chr9:95708192-96030392	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1054767	chr9:95738134-95875977	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1035230	chr9:95770249-95934982	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv893575	chr9:95781040-95854013	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv893576	chr9:95789960-96158277	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	esv1824329	chr9:95811604-95921347	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv893577	chr9:95812707-95872216	Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv893578	chr9:95818641-95887320	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16908779	C9orf3	cis	parietal	SCAN
rs16908779	GOT2	trans	cerebellum	SCAN
rs16908779	ZNF484	cis	cerebellum	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95824600-95854000	Weak transcription	Gastric	stomach
2	chr9:95834400-95857400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr9:95836200-95850000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr9:95836200-95855600	Weak transcription	Stomach Smooth Muscle	stomach
5	chr9:95838200-95851000	Strong transcription	Primary B cells from peripheral blood	blood
6	chr9:95839800-95851000	Weak transcription	K562	blood
7	chr9:95840400-95857000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr9:95844000-95853400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr9:95844800-95853400	Weak transcription	Colon Smooth Muscle	Colon
10	chr9:95845200-95857200	Weak transcription	Small Intestine	intestine
11	chr9:95845800-95854400	Weak transcription	Fetal Muscle Leg	muscle
12	chr9:95845800-95854800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr9:95846000-95852200	Strong transcription	Primary T cells from cord blood	blood
14	chr9:95846200-95849600	Strong transcription	Primary B cells from cord blood	blood
15	chr9:95846200-95850400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr9:95846200-95852000	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr9:95846200-95855000	Weak transcription	Fetal Lung	lung
18	chr9:95846400-95849600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr9:95846400-95849800	Strong transcription	Fetal Thymus	thymus
20	chr9:95846400-95851000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr9:95846400-95857000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr9:95846800-95849600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr9:95846800-95850600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr9:95846800-95851000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr9:95846800-95851600	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr9:95846800-95851600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr9:95847000-95851200	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr9:95847200-95851800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr9:95848000-95849600	ZNF genes & repeats	Fetal Intestine Small	intestine
30	chr9:95848400-95849600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr9:95848400-95850000	Weak transcription	GM12878-XiMat	blood
32	chr9:95848400-95851400	Strong transcription	Thymus	Thymus
33	chr9:95848400-95854000	Weak transcription	Fetal Stomach	stomach
34	chr9:95848400-95854600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr9:95848400-95854800	Weak transcription	Fetal Intestine Large	intestine
36	chr9:95848400-95855000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr9:95848400-95855000	Weak transcription	Duodenum Mucosa	Duodenum
38	chr9:95848400-95855400	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr9:95848400-95855800	Weak transcription	Liver	Liver
40	chr9:95848600-95855000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
41	chr9:95848600-95857000	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr9:95848800-95849800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr9:95848800-95855400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr9:95848800-95855600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr9:95849000-95849600	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr9:95849000-95849600	Enhancers	Stomach Mucosa	stomach
47	chr9:95849000-95849600	Genic enhancers	Spleen	Spleen
48	chr9:95849200-95849600	Enhancers	Colonic Mucosa	Colon
49	chr9:95849400-95851800	Weak transcription	Primary T helper cells PMA-I stimulated	--
50	chr9:95849400-95852000	Weak transcription	HepG2	liver

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