Variant report

Variant	rs4460498
Chromosome Location	chr9:100620412-100620413
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: 105 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10046805	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10113884	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10113907	0.84[AFR][1000 genomes]
rs10115216	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs10117642	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10119760	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10119795	0.80[CHB][hapmap];0.85[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes]
rs10119853	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10120412	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10122541	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10123699	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10512255	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs10739526	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs10759975	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10759981	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10818124	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10818133	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10818175	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10818213	0.82[EUR][1000 genomes]
rs10983853	0.86[CHB][hapmap]
rs10983855	0.86[CHB][hapmap]
rs10983958	0.88[ASN][1000 genomes]
rs10983959	0.88[ASN][1000 genomes]
rs10984103	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10984230	0.81[EUR][1000 genomes]
rs10984253	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs1156850	0.81[ASN][1000 genomes]
rs12004762	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs12006522	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs12238579	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs12341377	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12342417	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12343182	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12347191	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12348304	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12348691	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12550872	0.80[EUR][1000 genomes]
rs13287360	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13299924	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13300874	0.85[AFR][1000 genomes]
rs13302470	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1443434	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1443435	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1443436	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1561958	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs1561961	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs1867277	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1867278	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1867280	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1955143	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1955144	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1955145	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2120264	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2401639	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2417575	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2417576	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3021526	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3758248	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3758249	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3758251	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3808893	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs3824495	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs4255258	0.82[EUR][1000 genomes]
rs4297160	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4743139	0.89[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4743140	0.81[AFR][1000 genomes]
rs6478437	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6478445	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6478469	0.81[EUR][1000 genomes]
rs6478471	0.81[EUR][1000 genomes]
rs6586	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs7027221	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs7031386	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs7032086	0.80[EUR][1000 genomes]
rs7033315	0.85[AFR][1000 genomes]
rs7033765	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7034249	0.81[EUR][1000 genomes]
rs7034336	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs7034648	0.80[EUR][1000 genomes]
rs7036589	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs7037175	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7037324	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs7038998	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs7043516	0.90[YRI][hapmap];0.80[AFR][1000 genomes]
rs7044121	0.82[EUR][1000 genomes]
rs7044799	0.80[EUR][1000 genomes]
rs7045138	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7048255	0.81[EUR][1000 genomes]
rs7357707	0.85[AFR][1000 genomes]
rs7851552	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7851660	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7860144	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7866436	0.81[EUR][1000 genomes]
rs7868534	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7870540	0.81[ASN][1000 genomes]
rs7870795	0.93[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs874004	0.86[AFR][1000 genomes]
rs894673	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs907577	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs907581	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs925487	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9299258	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs993501	0.84[AMR][1000 genomes];0.86[EUR][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4460498	C9orf156	cis	Temporal Cortex	GTEx
rs4460498	C9orf156	cis	Frontal Cortex	GTEx
rs4460498	Hs.43687	cis	multi-tissue	Pritchard

Chromatin state (count:68 , 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	chr9:100619600-100620600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
7	chr9:100619600-100620800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
8	chr9:100619600-100621000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
9	chr9:100619800-100620600	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr9:100619800-100620600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr9:100619800-100620600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
12	chr9:100619800-100620800	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr9:100619800-100620800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
14	chr9:100619800-100620800	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr9:100619800-100620800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr9:100619800-100620800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
17	chr9:100619800-100620800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
18	chr9:100619800-100620800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
19	chr9:100619800-100620800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
20	chr9:100619800-100620800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
21	chr9:100619800-100620800	Bivalent Enhancer	Fetal Intestine Large	intestine
22	chr9:100619800-100620800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
23	chr9:100619800-100621000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
24	chr9:100620000-100620600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr9:100620000-100620800	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
26	chr9:100620000-100620800	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
27	chr9:100620000-100620800	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
28	chr9:100620000-100620800	Bivalent Enhancer	Left Ventricle	heart
29	chr9:100620000-100620800	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
30	chr9:100620200-100620600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
31	chr9:100620200-100620600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
32	chr9:100620200-100620600	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
33	chr9:100620200-100620600	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr9:100620200-100620600	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr9:100620200-100620600	Bivalent Enhancer	Psoas Muscle	Psoas
36	chr9:100620200-100620800	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr9:100620200-100620800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
38	chr9:100620200-100620800	Bivalent Enhancer	Primary hematopoietic stem cells	blood
39	chr9:100620200-100620800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
40	chr9:100620200-100620800	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
41	chr9:100620200-100620800	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
42	chr9:100620200-100620800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr9:100620200-100620800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr9:100620200-100620800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
45	chr9:100620200-100620800	Bivalent Enhancer	Fetal Brain Female	brain
46	chr9:100620200-100620800	Bivalent Enhancer	Fetal Muscle Leg	muscle
47	chr9:100620200-100620800	Enhancers	Right Atrium	heart
48	chr9:100620200-100621200	Enhancers	Spleen	Spleen
49	chr9:100620400-100620600	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr9:100620400-100620600	Bivalent Enhancer	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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