Variant report

Variant	rs9810460
Chromosome Location	chr3:179406597-179406598
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:179369821..179372060-chr3:179405523..179407102,2	MCF-7	breast:
2	chr3:179405760..179407669-chr3:179413822..179415850,2	MCF-7	breast:
3	chr3:179372827..179374690-chr3:179405067..179408048,2	K562	blood:
4	chr3:179380055..179381652-chr3:179404647..179407637,2	K562	blood:

Variant related genes	Relation type
ENSG00000058056	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs13097252	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13322033	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13326216	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2111391	0.80[LWK][hapmap]
rs2268941	0.93[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2268942	0.88[ASW][hapmap];0.93[CEU][hapmap];0.86[CHB][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2300767	0.80[LWK][hapmap]
rs34161332	0.95[ASN][1000 genomes]
rs34197007	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35934212	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4854945	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6771840	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.81[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6785332	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6788786	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6797965	1.00[CHB][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6807974	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71310390	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7629853	0.88[ASW][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];0.89[JPT][hapmap];0.97[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs800369	0.84[EUR][1000 genomes]
rs9810165	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9816744	0.87[CEU][hapmap];0.93[GIH][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes]
rs9859059	0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs9882786	0.80[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv4140	chr3:179383961-179429704	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9810460	AP2M1	cis	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179372600-179408400	Weak transcription	Fetal Intestine Small	intestine
2	chr3:179372600-179425200	Weak transcription	Primary hematopoietic stem cells	blood
3	chr3:179374600-179408000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr3:179380600-179418800	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr3:179384400-179410400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr3:179384800-179408000	Weak transcription	Fetal Thymus	thymus
7	chr3:179384800-179415200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr3:179384800-179425000	Weak transcription	Brain Anterior Caudate	brain
9	chr3:179384800-179428400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:179384800-179443800	Weak transcription	Esophagus	oesophagus
11	chr3:179385000-179415600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr3:179385000-179439200	Weak transcription	Brain Cingulate Gyrus	brain
13	chr3:179385000-179448400	Weak transcription	Fetal Brain Male	brain
14	chr3:179385400-179419000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:179390800-179408000	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr3:179391000-179444000	Weak transcription	Pancreas	Pancrea
17	chr3:179391000-179452200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:179391400-179415400	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr3:179391400-179426400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr3:179391400-179439200	Weak transcription	NHEK	skin
21	chr3:179391600-179408200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr3:179391600-179412800	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr3:179391600-179424000	Weak transcription	Hela-S3	cervix
24	chr3:179392600-179425000	Weak transcription	Aorta	Aorta
25	chr3:179394400-179415600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr3:179394400-179419400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr3:179396800-179407600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr3:179397000-179419200	Weak transcription	Liver	Liver
29	chr3:179397200-179423800	Weak transcription	HSMMtube	muscle
30	chr3:179397800-179439200	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr3:179398200-179408400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr3:179398400-179413600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr3:179398600-179421800	Weak transcription	Brain Substantia Nigra	brain
34	chr3:179399000-179426400	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr3:179399000-179434000	Weak transcription	A549	lung
36	chr3:179399000-179459800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr3:179399200-179425000	Weak transcription	Brain Germinal Matrix	brain
38	chr3:179399600-179409800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:179399600-179425000	Weak transcription	Lung	lung
40	chr3:179399800-179409000	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr3:179400000-179421600	Weak transcription	Brain Hippocampus Middle	brain
42	chr3:179400000-179424000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr3:179400600-179408400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr3:179400800-179426800	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr3:179401000-179406600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr3:179401200-179413600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr3:179401400-179408400	Weak transcription	Fetal Heart	heart
48	chr3:179401400-179424200	Weak transcription	Right Ventricle	heart
49	chr3:179401600-179415400	Weak transcription	Primary B cells from peripheral blood	blood
50	chr3:179402200-179409600	Strong transcription	Fetal Muscle Leg	muscle

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