Variant report

Variant	rs6771840
Chromosome Location	chr3:179415595-179415596
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:179405760..179407669-chr3:179413822..179415850,2	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1025864	0.81[JPT][hapmap]
rs13097252	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13322033	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13326216	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2111391	0.88[ASW][hapmap];0.81[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap]
rs2268941	0.93[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2268942	1.00[ASW][hapmap];0.93[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];0.97[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];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2300767	0.81[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap]
rs34197007	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35934212	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4854945	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs6785332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6788786	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs6797965	1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6807974	0.86[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs71310390	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7629853	0.86[CHB][hapmap];0.93[CHD][hapmap];0.84[LWK][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs800369	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9810165	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9810460	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]
rs9816744	0.87[CEU][hapmap];0.84[GIH][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs9882786	0.86[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
rs6771840	AP2M1	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179372600-179425200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr3:179380600-179418800	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr3:179384800-179425000	Weak transcription	Brain Anterior Caudate	brain
4	chr3:179384800-179428400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:179384800-179443800	Weak transcription	Esophagus	oesophagus
6	chr3:179385000-179415600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr3:179385000-179439200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr3:179385000-179448400	Weak transcription	Fetal Brain Male	brain
9	chr3:179385400-179419000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:179391000-179444000	Weak transcription	Pancreas	Pancrea
11	chr3:179391000-179452200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr3:179391400-179426400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr3:179391400-179439200	Weak transcription	NHEK	skin
14	chr3:179391600-179424000	Weak transcription	Hela-S3	cervix
15	chr3:179392600-179425000	Weak transcription	Aorta	Aorta
16	chr3:179394400-179415600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr3:179394400-179419400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr3:179397000-179419200	Weak transcription	Liver	Liver
19	chr3:179397200-179423800	Weak transcription	HSMMtube	muscle
20	chr3:179397800-179439200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr3:179398600-179421800	Weak transcription	Brain Substantia Nigra	brain
22	chr3:179399000-179426400	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr3:179399000-179434000	Weak transcription	A549	lung
24	chr3:179399000-179459800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr3:179399200-179425000	Weak transcription	Brain Germinal Matrix	brain
26	chr3:179399600-179425000	Weak transcription	Lung	lung
27	chr3:179400000-179421600	Weak transcription	Brain Hippocampus Middle	brain
28	chr3:179400000-179424000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr3:179400800-179426800	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr3:179401400-179424200	Weak transcription	Right Ventricle	heart
31	chr3:179402200-179425000	Weak transcription	Thymus	Thymus
32	chr3:179402200-179425200	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr3:179402600-179425000	Weak transcription	Fetal Intestine Large	intestine
34	chr3:179402600-179428600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr3:179402800-179421200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr3:179404000-179421400	Weak transcription	Primary B cells from cord blood	blood
37	chr3:179404000-179424000	Weak transcription	HepG2	liver
38	chr3:179404200-179422600	Weak transcription	Stomach Smooth Muscle	stomach
39	chr3:179404200-179425000	Weak transcription	Placenta	Placenta
40	chr3:179404400-179426600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr3:179404800-179426600	Weak transcription	GM12878-XiMat	blood
42	chr3:179405600-179419000	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr3:179405800-179429200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr3:179406000-179425000	Weak transcription	Fetal Brain Female	brain
45	chr3:179406200-179419200	Weak transcription	Primary T cells from cord blood	blood
46	chr3:179406200-179503000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr3:179406400-179415600	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr3:179406400-179418400	Weak transcription	Dnd41	blood
49	chr3:179406600-179449400	Weak transcription	Spleen	Spleen
50	chr3:179407000-179417600	Weak transcription	Fetal Lung	lung

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