Variant report

Variant	rs7628413
Chromosome Location	chr3:100479427-100479428
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:100477781..100481491-chr3:100485242..100489259,3	K562	blood:

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1012364	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10936343	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10936345	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10936346	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10936352	0.88[CEU][hapmap];0.91[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10936355	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12495397	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12496951	0.86[GIH][hapmap]
rs13059686	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13092027	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1402252	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1503845	0.83[GIH][hapmap]
rs1903744	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36194934	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3773922	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41373752	0.88[CEU][hapmap];0.91[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6441402	0.86[AMR][1000 genomes]
rs6775161	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6775789	0.88[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6777763	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6781584	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6784601	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6806786	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6810101	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7297	1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7614943	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7617184	0.96[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7629279	0.86[AMR][1000 genomes]
rs7642041	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs764684	0.81[CEU][hapmap];0.86[GIH][hapmap]
rs7650690	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7653531	0.85[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9811878	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9813835	0.82[AMR][1000 genomes]
rs9815749	0.86[AMR][1000 genomes]
rs9840505	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9849107	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9876383	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9879088	0.81[CEU][hapmap]
rs989795	0.84[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
rs7628413	TFG	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100450000-100501000	Weak transcription	Esophagus	oesophagus
2	chr3:100457200-100480200	Weak transcription	Brain Angular Gyrus	brain
3	chr3:100467400-100497600	Weak transcription	Fetal Intestine Small	intestine
4	chr3:100468200-100488600	Weak transcription	Colon Smooth Muscle	Colon
5	chr3:100469400-100480200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:100469800-100498200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr3:100469800-100501400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:100470200-100498400	Weak transcription	Right Ventricle	heart
9	chr3:100471000-100495800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:100471200-100480200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:100471600-100500400	Weak transcription	Lung	lung
12	chr3:100471800-100486200	Weak transcription	Brain Substantia Nigra	brain
13	chr3:100471800-100494600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:100471800-100502000	Weak transcription	Brain Anterior Caudate	brain
15	chr3:100472600-100484600	Weak transcription	NHEK	skin
16	chr3:100472800-100482800	Weak transcription	NHLF	lung
17	chr3:100472800-100494400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr3:100473000-100479800	Weak transcription	GM12878-XiMat	blood
19	chr3:100473000-100480400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr3:100473400-100480200	Weak transcription	A549	lung
21	chr3:100473400-100488400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr3:100473600-100480000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr3:100473600-100488600	Weak transcription	Fetal Muscle Trunk	muscle
24	chr3:100473600-100488800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr3:100473600-100489200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr3:100473800-100484600	Weak transcription	HMEC	breast
27	chr3:100473800-100496400	Weak transcription	Fetal Intestine Large	intestine
28	chr3:100474000-100488800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr3:100474200-100482400	Weak transcription	Stomach Smooth Muscle	stomach
30	chr3:100474400-100480600	Weak transcription	Primary T cells from cord blood	blood
31	chr3:100474400-100484800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr3:100474400-100494200	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr3:100474400-100500200	Weak transcription	HSMM	muscle
34	chr3:100474400-100501200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr3:100474800-100482800	Weak transcription	HSMMtube	muscle
36	chr3:100475000-100488000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr3:100475000-100499000	Weak transcription	Placenta	Placenta
38	chr3:100475600-100485600	Weak transcription	Left Ventricle	heart
39	chr3:100475600-100487600	Weak transcription	NHDF-Ad	bronchial
40	chr3:100475600-100520000	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr3:100477200-100480400	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr3:100477200-100484800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr3:100477400-100480400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr3:100477600-100480400	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr3:100477600-100480400	Enhancers	Fetal Muscle Leg	muscle
46	chr3:100477600-100480600	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr3:100477800-100482800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr3:100478000-100481200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr3:100478400-100480200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:100478400-100496600	Weak transcription	Aorta	Aorta

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