Variant report

Variant	rs6778945
Chromosome Location	chr3:119246827-119246828
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1060569	0.92[ASN][1000 genomes]
rs13080905	0.87[ASN][1000 genomes]
rs1797839	0.98[ASN][1000 genomes]
rs1900742	0.88[CHB][hapmap];0.88[ASN][1000 genomes]
rs1919586	0.88[CHB][hapmap];0.88[ASN][1000 genomes]
rs1919590	0.88[ASN][1000 genomes]
rs1967621	0.88[CHB][hapmap];0.85[CHD][hapmap];0.92[ASN][1000 genomes]
rs1976919	0.92[ASN][1000 genomes]
rs2177812	0.92[ASN][1000 genomes]
rs3732413	0.88[CHB][hapmap];0.87[CHD][hapmap];0.88[ASN][1000 genomes]
rs3814397	0.98[ASN][1000 genomes]
rs4687855	0.88[CHB][hapmap];0.87[CHD][hapmap];0.88[ASN][1000 genomes]
rs4687860	0.87[ASN][1000 genomes]
rs4688005	0.88[CHB][hapmap];0.87[CHD][hapmap];0.88[ASN][1000 genomes]
rs4688007	0.88[CHB][hapmap];0.87[CHD][hapmap];0.88[ASN][1000 genomes]
rs4688008	0.92[ASN][1000 genomes]
rs4688012	0.88[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs4688014	0.82[ASN][1000 genomes]
rs6414282	0.84[ASN][1000 genomes]
rs6414283	0.88[CHB][hapmap];0.87[CHD][hapmap];0.88[ASN][1000 genomes]
rs6438528	0.88[CHB][hapmap];0.82[CHD][hapmap];0.87[ASN][1000 genomes]
rs6438529	0.85[CHB][hapmap];0.87[CHD][hapmap];0.88[ASN][1000 genomes]
rs6438530	0.88[CHB][hapmap];0.88[ASN][1000 genomes]
rs6438531	0.88[CHB][hapmap];0.88[ASN][1000 genomes]
rs6438535	0.88[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs6762207	0.93[EUR][1000 genomes]
rs6776994	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs6777535	0.88[CHB][hapmap];0.87[ASN][1000 genomes]
rs6794822	0.84[ASN][1000 genomes]
rs6796970	0.88[ASN][1000 genomes]
rs727905	0.88[CHB][hapmap];0.87[CHD][hapmap];0.88[ASN][1000 genomes]
rs7427609	0.82[EUR][1000 genomes]
rs7430798	0.88[CHB][hapmap];0.87[ASN][1000 genomes]
rs7621259	0.92[ASN][1000 genomes]
rs7628626	0.88[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs7630587	0.88[ASN][1000 genomes]
rs7642502	0.88[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs9289129	0.88[CHB][hapmap];0.87[ASN][1000 genomes]
rs9809155	0.88[ASN][1000 genomes]
rs9836627	0.88[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs9850447	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9867768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9873196	0.85[CHB][hapmap];0.92[ASN][1000 genomes]
rs9874480	0.88[CHB][hapmap];0.88[ASN][1000 genomes]
rs9877854	0.88[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.92[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6778945	CD86	cis	cerebellum	SCAN
rs6778945	FSTL1	cis	cerebellum	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119228000-119250000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:119231800-119257200	Strong transcription	GM12878-XiMat	blood
3	chr3:119237800-119248000	Weak transcription	Aorta	Aorta
4	chr3:119237800-119251400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:119237800-119255800	Weak transcription	Spleen	Spleen
6	chr3:119238000-119248400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr3:119238200-119249000	Weak transcription	NHLF	lung
8	chr3:119239600-119248400	Weak transcription	HSMMtube	muscle
9	chr3:119239600-119253000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr3:119239800-119247400	Weak transcription	Fetal Heart	heart
11	chr3:119239800-119252400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr3:119240200-119248600	Weak transcription	Fetal Brain Male	brain
13	chr3:119240600-119247400	Strong transcription	Primary B cells from peripheral blood	blood
14	chr3:119240600-119249400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr3:119243000-119247400	Weak transcription	Brain Germinal Matrix	brain
16	chr3:119243000-119248600	Weak transcription	NHDF-Ad	bronchial
17	chr3:119243200-119251400	Weak transcription	Brain Hippocampus Middle	brain
18	chr3:119243400-119248400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr3:119243600-119247800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr3:119243600-119249400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr3:119243600-119250800	Weak transcription	Brain Anterior Caudate	brain
22	chr3:119243800-119248800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr3:119244000-119248200	Weak transcription	HSMM	muscle
24	chr3:119244200-119253400	Weak transcription	Brain Substantia Nigra	brain
25	chr3:119244400-119247600	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr3:119244400-119248200	Weak transcription	HMEC	breast
27	chr3:119244400-119248400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr3:119244400-119248400	Weak transcription	Osteobl	bone
29	chr3:119244600-119247200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr3:119244600-119248400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:119244600-119248400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr3:119244600-119248600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:119244600-119253200	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr3:119244800-119253400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr3:119244800-119257200	Weak transcription	Primary B cells from cord blood	blood
36	chr3:119245200-119247600	Weak transcription	Left Ventricle	heart
37	chr3:119245200-119248400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr3:119245200-119248400	Weak transcription	Fetal Lung	lung
39	chr3:119245200-119248600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:119245200-119248600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:119245200-119276600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr3:119245400-119247000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr3:119245400-119247000	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr3:119245400-119247000	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr3:119245400-119247000	Weak transcription	Thymus	Thymus
46	chr3:119245400-119247000	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr3:119245400-119247200	Weak transcription	Fetal Muscle Leg	muscle
48	chr3:119245400-119248200	Weak transcription	Placenta	Placenta
49	chr3:119245400-119253400	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr3:119246400-119247000	Enhancers	Gastric	stomach

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