Variant report

Variant	rs4854955
Chromosome Location	chr3:178918588-178918589
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:178913245..178916037-chr3:178916283..178918630,2	K562	blood:
2	chr3:178918266..178919818-chr3:178962428..178965232,2	MCF-7	breast:
3	chr3:178910913..178913212-chr3:178917675..178920478,2	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10936993	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12486399	0.94[EUR][1000 genomes]
rs12497857	0.90[EUR][1000 genomes]
rs13320527	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1517585	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2865084	1.00[CEU][hapmap];0.83[YRI][hapmap];0.94[EUR][1000 genomes]
rs28697961	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45455192	1.00[EUR][1000 genomes]
rs4854906	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4854940	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs4854976	0.94[EUR][1000 genomes]
rs4855094	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs4955793	1.00[GIH][hapmap];0.82[TSI][hapmap]
rs61404287	0.90[EUR][1000 genomes]
rs61796464	0.96[EUR][1000 genomes]
rs61796465	0.94[EUR][1000 genomes]
rs61796466	0.96[EUR][1000 genomes]
rs61796467	0.96[EUR][1000 genomes]
rs61798211	0.90[EUR][1000 genomes]
rs61798213	0.90[EUR][1000 genomes]
rs6443623	0.94[EUR][1000 genomes]
rs6791215	0.90[EUR][1000 genomes]
rs6804195	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs73051979	0.96[EUR][1000 genomes]
rs73054091	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7374077	0.86[EUR][1000 genomes]
rs7615259	0.94[EUR][1000 genomes]
rs950486	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9812252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9819654	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9823044	1.00[ASW][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9833206	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9860843	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9872959	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9878005	0.94[AMR][1000 genomes];0.96[EUR][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	nsv998253	chr3:178622707-179196274	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv536814	chr3:178622707-179196274	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv3354111	chr3:178833305-179156908	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:178897800-178919400	Weak transcription	Fetal Intestine Small	intestine
2	chr3:178899200-178951800	Weak transcription	K562	blood
3	chr3:178900000-178929800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:178904000-178918600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:178906400-178962400	Weak transcription	HepG2	liver
6	chr3:178908000-178919800	Weak transcription	Brain Angular Gyrus	brain
7	chr3:178908000-178923600	Weak transcription	Fetal Brain Female	brain
8	chr3:178908800-178920000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:178908800-178922800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:178909000-178919800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr3:178909000-178931400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:178909000-178947000	Weak transcription	Ovary	ovary
13	chr3:178909400-178918800	Weak transcription	Fetal Muscle Leg	muscle
14	chr3:178909400-178925400	Weak transcription	Aorta	Aorta
15	chr3:178910000-178919400	Weak transcription	Fetal Stomach	stomach
16	chr3:178911000-178919600	Weak transcription	Placenta	Placenta
17	chr3:178911200-178953400	Weak transcription	Gastric	stomach
18	chr3:178911400-178919400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr3:178912400-178919600	Weak transcription	Spleen	Spleen
20	chr3:178912400-178924000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr3:178912400-178978600	Weak transcription	Right Ventricle	heart
22	chr3:178912600-178919600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:178912600-178947800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:178913000-178918600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr3:178913000-178919600	Weak transcription	Fetal Intestine Large	intestine
26	chr3:178913000-178925000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:178913000-178925400	Weak transcription	Pancreas	Pancrea
28	chr3:178913000-178930800	Weak transcription	Left Ventricle	heart
29	chr3:178913000-178948200	Weak transcription	Psoas Muscle	Psoas
30	chr3:178913200-178918600	Weak transcription	Liver	Liver
31	chr3:178913200-178945200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr3:178913200-178947000	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr3:178913200-178947000	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr3:178913800-178918600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr3:178913800-178919600	Weak transcription	Brain Germinal Matrix	brain
36	chr3:178913800-178954000	Weak transcription	Fetal Heart	heart
37	chr3:178913800-178969000	Weak transcription	Small Intestine	intestine
38	chr3:178914000-178918600	Weak transcription	Fetal Lung	lung
39	chr3:178914000-178918800	Weak transcription	Primary hematopoietic stem cells	blood
40	chr3:178914000-178919600	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr3:178914000-178919600	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr3:178914000-178921400	Weak transcription	Fetal Kidney	kidney
43	chr3:178914000-178928200	Weak transcription	Brain Hippocampus Middle	brain
44	chr3:178914200-178918800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr3:178914200-178928000	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr3:178914200-178928000	Weak transcription	Brain Substantia Nigra	brain
47	chr3:178914200-178928200	Weak transcription	Brain Anterior Caudate	brain
48	chr3:178914400-178918600	Weak transcription	Duodenum Mucosa	Duodenum
49	chr3:178914600-178918600	Weak transcription	Primary T cells from cord blood	blood
50	chr3:178914600-178919600	Weak transcription	Skeletal Muscle Female	skeletal muscle

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