Variant report

Variant	rs648353
Chromosome Location	chr9:136822827-136822828
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:136822394..136827953-chr9:136855901..136860268,9	MCF-7	breast:
2	chr9:136821303..136824220-chr9:136826571..136828241,2	MCF-7	breast:
3	chr9:136821904..136824368-chr9:136852633..136855112,2	MCF-7	breast:
4	chr9:136817340..136820147-chr9:136822604..136825397,2	MCF-7	breast:
5	chr9:136815263..136820961-chr9:136821414..136825553,6	MCF-7	breast:
6	chr9:136737400..136743457-chr9:136819359..136829756,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160293	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1633763	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1633764	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2319056	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs471882	0.84[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.84[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs478393	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs481964	1.00[JPT][hapmap]
rs524538	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs526581	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs527316	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs557327	0.90[JPT][hapmap]
rs561257	0.90[JPT][hapmap]
rs567208	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs619173	0.90[JPT][hapmap]
rs621569	0.90[JPT][hapmap]
rs62576939	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs635277	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs635323	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs635739	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs636651	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs653373	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs688091	0.90[JPT][hapmap]
rs694511	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894123	chr9:136682408-136852501	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv894124	chr9:136716399-136870787	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv894125	chr9:136723520-136931957	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats 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	31 gene(s)	inside rSNPs	diseases
4	nsv894128	chr9:136753246-136906752	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv1046310	chr9:136762829-136872226	Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv894130	chr9:136767346-136906752	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv831748	chr9:136788484-136944326	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats 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	30 gene(s)	inside rSNPs	diseases
8	nsv894131	chr9:136792765-136906752	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv466626	chr9:136807770-136835343	Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv615742	chr9:136807770-136835343	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv831749	chr9:136809200-136915764	Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
12	nsv894132	chr9:136813341-136950691	Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
13	nsv982642	chr9:136819005-136837069	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	esv2761297	chr9:136819288-136825744	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs648353	C9orf163	cis	cerebellum	SCAN
rs648353	PNMA1	trans	parietal	SCAN
rs648353	C9orf98	cis	cerebellum	SCAN
rs648353	C9orf50	cis	parietal	SCAN
rs648353	AGPAT2	cis	cerebellum	SCAN
rs648353	MED27	cis	parietal	SCAN

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:136817000-136824400	Weak transcription	HepG2	liver
2	chr9:136818200-136823200	Enhancers	Spleen	Spleen
3	chr9:136818600-136823200	Enhancers	Fetal Muscle Leg	muscle
4	chr9:136819000-136823200	Enhancers	Fetal Thymus	thymus
5	chr9:136819000-136823200	Enhancers	Lung	lung
6	chr9:136819400-136823000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr9:136819400-136823000	Enhancers	Fetal Brain Female	brain
8	chr9:136819400-136823200	Enhancers	H1 Cell Line	embryonic stem cell
9	chr9:136819400-136823200	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr9:136819400-136823200	Enhancers	Placenta	Placenta
11	chr9:136819800-136823200	Enhancers	H9 Cell Line	embryonic stem cell
12	chr9:136819800-136823200	Enhancers	Fetal Muscle Trunk	muscle
13	chr9:136819800-136823200	Enhancers	Pancreas	Pancrea
14	chr9:136820800-136823000	Enhancers	Left Ventricle	heart
15	chr9:136820800-136823200	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr9:136821000-136823000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr9:136821000-136823000	Enhancers	Fetal Lung	lung
18	chr9:136821000-136823000	Flanking Active TSS	GM12878-XiMat	blood
19	chr9:136821000-136823200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr9:136821000-136823200	Enhancers	Placenta Amnion	Placenta Amnion
21	chr9:136821000-136823200	Enhancers	HMEC	breast
22	chr9:136821000-136823800	Enhancers	NHEK	skin
23	chr9:136821200-136823000	Enhancers	Osteobl	bone
24	chr9:136821400-136823000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
25	chr9:136821400-136823000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
26	chr9:136821400-136823200	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr9:136821400-136823200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr9:136821400-136823200	Enhancers	Duodenum Mucosa	Duodenum
29	chr9:136821400-136823800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr9:136821600-136823000	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr9:136821600-136823000	Enhancers	Primary hematopoietic stem cells	blood
32	chr9:136821600-136823000	Genic enhancers	Fetal Intestine Small	intestine
33	chr9:136821600-136823000	Enhancers	NH-A	brain
34	chr9:136821600-136823200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr9:136821600-136823200	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr9:136821600-136823200	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr9:136821600-136823200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr9:136821600-136823200	Enhancers	Rectal Mucosa Donor 29	rectum
39	chr9:136821800-136823200	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr9:136821800-136823200	Enhancers	HUVEC	blood vessel
41	chr9:136821800-136823800	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr9:136821800-136828600	Enhancers	Primary B cells from cord blood	blood
43	chr9:136822000-136823000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr9:136822000-136823000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr9:136822000-136823000	Enhancers	Muscle Satellite Cultured Cells	--
46	chr9:136822000-136823000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr9:136822000-136823000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
48	chr9:136822000-136823200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr9:136822000-136823200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr9:136822000-136823200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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