Variant report

Variant	rs2994369
Chromosome Location	chr9:96366513-96366514
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	chr9:96365988..96367962-chr9:96372230..96374229,2	MCF-7	breast:
2	chr9:96363027..96365894-chr9:96366005..96367741,2	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1000850	0.82[CHD][hapmap]
rs1000852	0.85[CHD][hapmap]
rs10122092	0.83[CHD][hapmap]
rs10821170	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10821171	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10821172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10821177	1.00[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];1.00[ASN][1000 genomes]
rs10992794	0.92[ASN][1000 genomes]
rs10992795	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10992796	0.89[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.92[LWK][hapmap];0.88[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13290276	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs13296529	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17533702	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2254712	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2265300	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2265574	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2265575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2265576	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2989752	1.00[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]
rs2989753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2989755	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2989756	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2994365	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2994370	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs4073155	0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs4743929	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4744255	0.87[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.92[ASN][1000 genomes]
rs4744258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4744259	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56351334	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs62573991	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs62574558	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs928368	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9409477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9644969	0.85[CHD][hapmap]

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	nsv824984	chr9:96310933-96375022	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1040891	chr9:96361529-96397338	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1044461	chr9:96362048-96397338	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv893585	chr9:96363859-96403367	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv893586	chr9:96363859-96493773	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2994369	C9orf21	cis	cerebellum	SCAN
rs2994369	FAM120AOS	Cis_1M	lymphoblastoid	RTeQTL
rs2994369	PTCH1	cis	parietal	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96352400-96369200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr9:96352400-96384600	Weak transcription	NHLF	lung
3	chr9:96357000-96367000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr9:96361000-96369400	Weak transcription	Dnd41	blood
5	chr9:96361400-96372000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr9:96361400-96380400	Weak transcription	Fetal Brain Male	brain
7	chr9:96361600-96379400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr9:96363000-96368600	Weak transcription	Fetal Lung	lung
9	chr9:96363200-96366600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr9:96363200-96367400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:96363200-96367400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr9:96363200-96367600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr9:96363200-96367600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr9:96363200-96368000	Weak transcription	Adipose Nuclei	Adipose
15	chr9:96363200-96368800	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr9:96363200-96369000	Weak transcription	Brain Anterior Caudate	brain
17	chr9:96363200-96374200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr9:96363200-96374600	Weak transcription	Gastric	stomach
19	chr9:96363200-96392000	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr9:96363400-96366600	Strong transcription	Fetal Intestine Small	intestine
21	chr9:96363400-96367400	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr9:96363400-96367600	Weak transcription	Primary B cells from cord blood	blood
23	chr9:96363400-96368600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr9:96363600-96367200	Weak transcription	Fetal Intestine Large	intestine
25	chr9:96363600-96367800	Weak transcription	Primary hematopoietic stem cells	blood
26	chr9:96363600-96367800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr9:96363600-96383600	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr9:96363800-96367600	Weak transcription	Primary T cells from cord blood	blood
29	chr9:96363800-96374000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr9:96363800-96374400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr9:96364000-96368800	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr9:96364200-96369200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr9:96364200-96380600	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr9:96365000-96366600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr9:96365200-96366600	Enhancers	Fetal Muscle Trunk	muscle
36	chr9:96365200-96366600	Enhancers	Psoas Muscle	Psoas
37	chr9:96365200-96366600	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr9:96365200-96366600	Enhancers	Spleen	Spleen
39	chr9:96365200-96367800	Weak transcription	Primary B cells from peripheral blood	blood
40	chr9:96365400-96366600	Enhancers	Left Ventricle	heart
41	chr9:96365400-96366600	Enhancers	Lung	lung
42	chr9:96365800-96366600	Enhancers	Right Ventricle	heart
43	chr9:96366000-96366600	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr9:96366000-96366600	Enhancers	Fetal Heart	heart
45	chr9:96366000-96366600	Enhancers	Stomach Smooth Muscle	stomach
46	chr9:96366000-96374600	Weak transcription	Rectal Smooth Muscle	rectum
47	chr9:96366200-96366600	Enhancers	Fetal Muscle Leg	muscle
48	chr9:96366200-96366600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
49	chr9:96366200-96367400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr9:96366200-96375000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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