Variant report

Variant	rs1465965
Chromosome Location	chr9:100620326-100620327
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:100619175..100621925-chr9:100624139..100627052,3	K562	blood:
2	chr9:100602066..100604948-chr9:100618492..100620676,2	K562	blood:
3	chr9:100616472..100617973-chr9:100620292..100623040,2	K562	blood:
4	chr9:100619175..100621925-chr9:100624139..100625780,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10116976	1.00[CHB][hapmap]
rs10123699	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10739513	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759960	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10760011	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10760017	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10983975	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13287360	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1348386	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1867279	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1912998	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3021523	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743138	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4743139	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6478423	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7024345	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7046645	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7048394	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7848950	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7849497	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7859751	0.91[CEU][hapmap];0.81[AMR][1000 genomes]
rs7870540	0.81[AMR][1000 genomes]
rs7870795	0.91[CEU][hapmap];0.81[AMR][1000 genomes]
rs7870871	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs894672	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs907576	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs907578	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs907579	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs907580	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs907582	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs925485	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs925486	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs925487	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs973473	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893611	chr9:100561055-100739888	Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv6627	chr9:100576258-100621034	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1465965	C9orf156	cis	Temporal Cortex	GTEx

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100619200-100620800	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:100619200-100620800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
3	chr9:100619200-100620800	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
4	chr9:100619400-100620800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
5	chr9:100619400-100620800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr9:100619600-100620400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr9:100619600-100620600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
8	chr9:100619600-100620800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
9	chr9:100619600-100621000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
10	chr9:100619800-100620400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
11	chr9:100619800-100620400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr9:100619800-100620400	Bivalent Enhancer	Fetal Intestine Small	intestine
13	chr9:100619800-100620600	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr9:100619800-100620600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr9:100619800-100620600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
16	chr9:100619800-100620800	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr9:100619800-100620800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
18	chr9:100619800-100620800	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr9:100619800-100620800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr9:100619800-100620800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
21	chr9:100619800-100620800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
22	chr9:100619800-100620800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
23	chr9:100619800-100620800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
24	chr9:100619800-100620800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
25	chr9:100619800-100620800	Bivalent Enhancer	Fetal Intestine Large	intestine
26	chr9:100619800-100620800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
27	chr9:100619800-100621000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
28	chr9:100620000-100620400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
29	chr9:100620000-100620400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr9:100620000-100620400	Bivalent Enhancer	Lung	lung
31	chr9:100620000-100620400	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
32	chr9:100620000-100620600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr9:100620000-100620800	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
34	chr9:100620000-100620800	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
35	chr9:100620000-100620800	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
36	chr9:100620000-100620800	Bivalent Enhancer	Left Ventricle	heart
37	chr9:100620000-100620800	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
38	chr9:100620200-100620400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr9:100620200-100620400	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
40	chr9:100620200-100620400	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr9:100620200-100620400	Bivalent Enhancer	Liver	Liver
42	chr9:100620200-100620400	Bivalent Enhancer	HepG2	liver
43	chr9:100620200-100620600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
44	chr9:100620200-100620600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
45	chr9:100620200-100620600	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
46	chr9:100620200-100620600	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr9:100620200-100620600	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr9:100620200-100620600	Bivalent Enhancer	Psoas Muscle	Psoas
49	chr9:100620200-100620800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr9:100620200-100620800	Bivalent Enhancer	Primary B cells from peripheral blood	blood

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