Variant report

Variant	rs1599796
Chromosome Location	chr3:119243934-119243935
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119187617..119189310-chr3:119243541..119246268,2	MCF-7	breast:
2	chr3:119237156..119239321-chr3:119242706..119244832,2	K562	blood:
3	chr3:119243668..119244299-chr3:119278300..119279020,3	MCF-7	breast:
4	chr3:119243377..119244472-chr3:119399849..119400744,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000121594	Chromatin interaction
ENSG00000176142	Chromatin interaction
ENSG00000163389	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11706028	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11706042	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11707612	0.94[ASN][1000 genomes]
rs11709468	0.94[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs11714738	0.99[ASN][1000 genomes]
rs11714843	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11719448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720158	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720423	0.94[ASN][1000 genomes]
rs1599795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16829789	0.84[GIH][hapmap]
rs17203104	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17203188	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1938	0.94[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs1961132	0.99[ASN][1000 genomes]
rs2049500	0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs2276713	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2280670	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2293371	0.96[ASN][1000 genomes]
rs34090996	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3732418	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3755579	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4447803	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs4461452	0.94[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs4687851	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4687854	0.93[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4687863	0.94[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs4688002	0.87[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4688009	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4688011	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4688013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57506457	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59024323	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60938951	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62263399	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62263404	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62263406	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62263444	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62264483	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62264487	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6438534	0.91[ASN][1000 genomes]
rs6788474	0.91[ASN][1000 genomes]
rs7610335	0.93[ASN][1000 genomes]
rs9289131	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9832341	0.98[ASN][1000 genomes]
rs9850413	0.91[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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer 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	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829695	chr3:119178890-119367996	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1599796	CD80	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119220200-119246800	Weak transcription	Stomach Mucosa	stomach
2	chr3:119221000-119244600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr3:119221200-119244400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr3:119221400-119245400	Strong transcription	Placenta	Placenta
5	chr3:119221600-119244600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:119222000-119245400	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr3:119224000-119245200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr3:119226000-119245200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:119226000-119245200	Strong transcription	Liver	Liver
10	chr3:119226600-119245200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:119227400-119245400	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr3:119228000-119250000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr3:119229200-119244600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr3:119230600-119245400	Strong transcription	Rectal Mucosa Donor 29	rectum
15	chr3:119230800-119244400	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr3:119231200-119244000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr3:119231800-119244000	Strong transcription	Adipose Nuclei	Adipose
18	chr3:119231800-119244800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr3:119231800-119245400	Strong transcription	Skeletal Muscle Female	skeletal muscle
20	chr3:119231800-119257200	Strong transcription	GM12878-XiMat	blood
21	chr3:119232000-119244200	Strong transcription	Primary T helper cells PMA-I stimulated	--
22	chr3:119232000-119244200	Strong transcription	Brain Substantia Nigra	brain
23	chr3:119232000-119245200	Strong transcription	A549	lung
24	chr3:119233000-119245200	Strong transcription	Duodenum Mucosa	Duodenum
25	chr3:119233200-119244600	Strong transcription	Brain Inferior Temporal Lobe	brain
26	chr3:119234400-119244600	Strong transcription	Fetal Intestine Large	intestine
27	chr3:119234600-119244400	Strong transcription	Rectal Mucosa Donor 31	rectum
28	chr3:119237600-119245200	Strong transcription	Fetal Thymus	thymus
29	chr3:119237800-119244800	Weak transcription	Hela-S3	cervix
30	chr3:119237800-119245000	Weak transcription	Colonic Mucosa	Colon
31	chr3:119237800-119245400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr3:119237800-119245800	Weak transcription	Small Intestine	intestine
33	chr3:119237800-119246000	Weak transcription	Right Ventricle	heart
34	chr3:119237800-119246400	Weak transcription	Pancreas	Pancrea
35	chr3:119237800-119246600	Weak transcription	Esophagus	oesophagus
36	chr3:119237800-119248000	Weak transcription	Aorta	Aorta
37	chr3:119237800-119251400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr3:119237800-119255800	Weak transcription	Spleen	Spleen
39	chr3:119238000-119245000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:119238000-119245200	Strong transcription	Dnd41	blood
41	chr3:119238000-119245400	Strong transcription	Fetal Muscle Leg	muscle
42	chr3:119238000-119248400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:119238200-119245200	Weak transcription	Brain Cingulate Gyrus	brain
44	chr3:119238200-119245200	Strong transcription	Fetal Lung	lung
45	chr3:119238200-119245800	Weak transcription	NHEK	skin
46	chr3:119238200-119249000	Weak transcription	NHLF	lung
47	chr3:119238400-119244400	Strong transcription	Fetal Muscle Trunk	muscle
48	chr3:119238600-119244200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr3:119238800-119246800	Weak transcription	Rectal Smooth Muscle	rectum
50	chr3:119239600-119244000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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