Variant report

Variant	rs10821171
Chromosome Location	chr9:96362235-96362236
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:96356589..96359432-chr9:96360730..96362532,3	MCF-7	breast:
2	chr9:96360523..96363170-chr9:96791187..96793107,2	MCF-7	breast:
3	chr13:19663485..19664146-chr9:96361818..96362350,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000158079	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10761237	0.81[CHB][hapmap]
rs10821170	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10821172	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10821177	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10992794	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10992795	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10992796	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13290276	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13296529	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs17533702	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2254712	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2265300	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2265574	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2265575	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2265576	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2989752	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]
rs2989753	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2989755	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2989756	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2994365	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2994369	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]
rs2994370	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]
rs4073155	0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs4743929	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4744255	0.86[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs4744258	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4744259	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56351334	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62573991	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62574558	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs928368	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9409477	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10821171	FAM120AOS	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96345000-96362600	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr9:96349000-96365800	Weak transcription	Rectal Smooth Muscle	rectum
3	chr9:96352400-96366000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr9:96352400-96369200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr9:96352400-96384600	Weak transcription	NHLF	lung
6	chr9:96352600-96362400	Weak transcription	Fetal Lung	lung
7	chr9:96355200-96362600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:96355200-96362800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr9:96355200-96362800	Weak transcription	Brain Angular Gyrus	brain
10	chr9:96356400-96364000	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr9:96356600-96365600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr9:96356800-96362600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr9:96357000-96362400	Weak transcription	HSMM	muscle
14	chr9:96357000-96362600	Weak transcription	A549	lung
15	chr9:96357000-96367000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr9:96357200-96362400	Weak transcription	Hela-S3	cervix
17	chr9:96357200-96362800	Weak transcription	HMEC	breast
18	chr9:96357400-96362400	Weak transcription	NHEK	skin
19	chr9:96357600-96364200	Enhancers	Pancreas	Pancrea
20	chr9:96357600-96364600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr9:96357800-96362600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr9:96358200-96363000	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr9:96358200-96363600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr9:96358400-96363000	Enhancers	Right Atrium	heart
25	chr9:96358400-96364000	Enhancers	Skeletal Muscle Male	skeletal muscle
26	chr9:96358400-96365200	Enhancers	Primary B cells from peripheral blood	blood
27	chr9:96359200-96364000	Enhancers	Primary T cells fromperipheralblood	blood
28	chr9:96359400-96362600	Enhancers	Primary T cells from cord blood	blood
29	chr9:96359600-96363000	Enhancers	Ovary	ovary
30	chr9:96359600-96363200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr9:96359600-96363200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
32	chr9:96359600-96363600	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr9:96359600-96363800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr9:96359600-96363800	Enhancers	Sigmoid Colon	Sigmoid Colon
35	chr9:96359600-96364200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr9:96359600-96364200	Enhancers	Lung	lung
37	chr9:96359600-96364400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr9:96359600-96364400	Enhancers	Left Ventricle	heart
39	chr9:96359800-96363200	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr9:96359800-96363400	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr9:96359800-96363600	Enhancers	Fetal Thymus	thymus
42	chr9:96360000-96363000	Enhancers	Fetal Brain Female	brain
43	chr9:96360000-96363600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr9:96360000-96363600	Enhancers	Brain Substantia Nigra	brain
45	chr9:96360000-96364000	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr9:96360000-96365000	Enhancers	Brain Germinal Matrix	brain
47	chr9:96360200-96363200	Enhancers	Brain Hippocampus Middle	brain
48	chr9:96360200-96363200	Enhancers	Placenta	Placenta
49	chr9:96360200-96363400	Genic enhancers	Fetal Intestine Small	intestine
50	chr9:96360200-96363600	Enhancers	Fetal Intestine Large	intestine

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