Variant report

Variant	rs3021523
Chromosome Location	chr9:100616583-100616584
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:100616472..100617973-chr9:100620292..100623040,2	K562	blood:

Extended variants
information (count: 39 )
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	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10759960	0.87[AMR][1000 genomes];0.84[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	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1465965	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1867279	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1912998	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4743139	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6478423	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7024345	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7046645	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7048394	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7848950	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7849497	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[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];0.86[EUR][1000 genomes]
rs894672	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs907576	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs907578	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs907579	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs907580	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs907582	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs925485	0.91[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs925486	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs925487	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs973473	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
3	nsv825000	chr9:100613121-100618319	Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv3330300	chr9:100613506-100618154	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv3421459	chr9:100614656-100617704	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3021523	C9orf156	cis	Temporal Cortex	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100613400-100618800	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr9:100613600-100618000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr9:100613800-100616600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr9:100613800-100616800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr9:100613800-100617400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
6	chr9:100613800-100617800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
7	chr9:100614000-100616600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
8	chr9:100614000-100617800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
9	chr9:100614000-100617800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr9:100614600-100616600	Bivalent Enhancer	Placenta	Placenta
11	chr9:100614800-100616600	Flanking Bivalent TSS/Enh	Right Ventricle	heart
12	chr9:100615000-100616600	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
13	chr9:100615000-100616800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
14	chr9:100615000-100617000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr9:100615000-100617000	Bivalent/Poised TSS	NHEK	skin
16	chr9:100615200-100616600	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
17	chr9:100615200-100616800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
18	chr9:100615200-100617000	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr9:100615200-100617000	Bivalent/Poised TSS	HSMM	muscle
20	chr9:100615200-100617200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr9:100615400-100616600	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
22	chr9:100615400-100616600	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr9:100615400-100616600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr9:100615400-100616600	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr9:100615400-100616600	Flanking Active TSS	Pancreas	Pancrea
26	chr9:100615400-100616600	Flanking Bivalent TSS/Enh	HMEC	breast
27	chr9:100615400-100616800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr9:100615600-100616600	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr9:100615600-100616600	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr9:100615600-100616600	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
31	chr9:100615600-100616600	Bivalent/Poised TSS	GM12878-XiMat	blood
32	chr9:100615600-100616600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
33	chr9:100615600-100616800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
34	chr9:100615600-100616800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr9:100615600-100616800	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
36	chr9:100615600-100617000	Active TSS	A549	lung
37	chr9:100615600-100617200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr9:100615600-100617400	Active TSS	Hela-S3	cervix
39	chr9:100615800-100616600	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr9:100615800-100616600	Flanking Active TSS	Primary hematopoietic stem cells	blood
41	chr9:100615800-100616600	Bivalent/Poised TSS	Primary T killer memory cells from peripheral blood	blood
42	chr9:100615800-100616600	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
43	chr9:100615800-100616600	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
44	chr9:100615800-100616600	Bivalent/Poised TSS	HSMMtube	muscle
45	chr9:100615800-100616800	Bivalent/Poised TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr9:100615800-100617200	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
47	chr9:100616000-100616600	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr9:100616000-100616600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr9:100616000-100616600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
50	chr9:100616000-100616600	Bivalent/Poised TSS	Primary T killer naive cells fromperipheralblood	blood

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