Variant report

Variant	rs560803
Chromosome Location	chr3:100479265-100479266
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	chr3:100476994..100479281-chr3:100486300..100488381,2	K562	blood:
2	chr3:100477781..100481491-chr3:100485242..100489259,3	K562	blood:

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10755119	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[ASN][1000 genomes]
rs10936349	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11353	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1143774	0.82[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1143776	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1144105	1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1144106	1.00[CHB][hapmap];0.90[TSI][hapmap];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1144107	1.00[CHB][hapmap];0.83[CHD][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1144108	1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1144122	1.00[CHB][hapmap];0.83[CHD][hapmap];0.86[TSI][hapmap];1.00[ASN][1000 genomes]
rs1144124	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1144125	1.00[CHB][hapmap];0.83[CHD][hapmap];0.86[TSI][hapmap];1.00[ASN][1000 genomes]
rs1144126	1.00[CHB][hapmap];0.83[CHD][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1145348	1.00[CHB][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1145351	1.00[ASN][1000 genomes]
rs1165250	0.80[AMR][1000 genomes]
rs1165253	1.00[ASN][1000 genomes]
rs1165255	1.00[ASN][1000 genomes]
rs1165260	1.00[ASN][1000 genomes]
rs1165264	1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1165534	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11921801	1.00[CHB][hapmap]
rs11921907	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1384198	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1520652	1.00[ASN][1000 genomes]
rs1620897	1.00[ASN][1000 genomes]
rs1623413	1.00[ASN][1000 genomes]
rs1628469	0.82[AMR][1000 genomes]
rs1676339	1.00[ASN][1000 genomes]
rs1676343	1.00[CHB][hapmap]
rs1676345	1.00[ASN][1000 genomes]
rs1676346	1.00[ASN][1000 genomes]
rs1676349	1.00[ASN][1000 genomes]
rs1676366	1.00[ASN][1000 genomes]
rs1680520	1.00[ASN][1000 genomes]
rs1718272	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1718273	1.00[ASN][1000 genomes]
rs1718278	1.00[ASN][1000 genomes]
rs1718279	1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2126540	0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2461498	1.00[ASN][1000 genomes]
rs4088588	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4144968	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4928070	1.00[CHB][hapmap];0.83[CHD][hapmap];0.82[TSI][hapmap];1.00[ASN][1000 genomes]
rs4928087	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs586347	1.00[CHB][hapmap]
rs591728	1.00[CHB][hapmap];0.83[CHD][hapmap];0.88[TSI][hapmap];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs603630	1.00[ASN][1000 genomes]
rs605300	1.00[ASN][1000 genomes]
rs610854	1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs629091	1.00[ASN][1000 genomes]
rs6441383	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6441384	1.00[CHB][hapmap]
rs6441552	0.83[CEU][hapmap]
rs653002	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs670008	1.00[CHB][hapmap]
rs6767460	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6770559	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6779489	1.00[CHB][hapmap]
rs6789364	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs694612	1.00[ASN][1000 genomes]
rs7635652	0.83[AMR][1000 genomes]
rs7637250	0.83[AMR][1000 genomes]
rs7637272	0.86[AMR][1000 genomes]
rs7644599	1.00[ASN][1000 genomes]
rs900234	0.83[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9864288	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs9878163	1.00[CHB][hapmap]

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	esv2751969	chr3:100312499-100479384	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	esv2751972	chr3:100342493-100493062	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv432469	chr3:100342493-100493062	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs560803	TFG	cis	multi-tissue	Pritchard

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100441000-100479400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:100450000-100501000	Weak transcription	Esophagus	oesophagus
3	chr3:100457200-100480200	Weak transcription	Brain Angular Gyrus	brain
4	chr3:100467400-100497600	Weak transcription	Fetal Intestine Small	intestine
5	chr3:100468200-100488600	Weak transcription	Colon Smooth Muscle	Colon
6	chr3:100469400-100480200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:100469800-100498200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr3:100469800-100501400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr3:100470200-100498400	Weak transcription	Right Ventricle	heart
10	chr3:100471000-100495800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr3:100471200-100480200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:100471600-100500400	Weak transcription	Lung	lung
13	chr3:100471800-100479400	Weak transcription	Fetal Kidney	kidney
14	chr3:100471800-100486200	Weak transcription	Brain Substantia Nigra	brain
15	chr3:100471800-100494600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr3:100471800-100502000	Weak transcription	Brain Anterior Caudate	brain
17	chr3:100472600-100484600	Weak transcription	NHEK	skin
18	chr3:100472800-100482800	Weak transcription	NHLF	lung
19	chr3:100472800-100494400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr3:100473000-100479800	Weak transcription	GM12878-XiMat	blood
21	chr3:100473000-100480400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr3:100473400-100480200	Weak transcription	A549	lung
23	chr3:100473400-100488400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr3:100473600-100480000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr3:100473600-100488600	Weak transcription	Fetal Muscle Trunk	muscle
26	chr3:100473600-100488800	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr3:100473600-100489200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr3:100473800-100484600	Weak transcription	HMEC	breast
29	chr3:100473800-100496400	Weak transcription	Fetal Intestine Large	intestine
30	chr3:100474000-100488800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr3:100474200-100482400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr3:100474400-100480600	Weak transcription	Primary T cells from cord blood	blood
33	chr3:100474400-100484800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr3:100474400-100494200	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr3:100474400-100500200	Weak transcription	HSMM	muscle
36	chr3:100474400-100501200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr3:100474800-100482800	Weak transcription	HSMMtube	muscle
38	chr3:100475000-100488000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr3:100475000-100499000	Weak transcription	Placenta	Placenta
40	chr3:100475600-100485600	Weak transcription	Left Ventricle	heart
41	chr3:100475600-100487600	Weak transcription	NHDF-Ad	bronchial
42	chr3:100475600-100520000	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr3:100475800-100479400	Weak transcription	Adipose Nuclei	Adipose
44	chr3:100477200-100480400	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr3:100477200-100484800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr3:100477400-100480400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr3:100477600-100479400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr3:100477600-100480400	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr3:100477600-100480400	Enhancers	Fetal Muscle Leg	muscle
50	chr3:100477600-100480600	Weak transcription	HUES64 Cell Line	embryonic stem cell

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