Variant report

Variant	rs2516839
Chromosome Location	chr1:161013121-161013122
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:161013120-161013270	A549	lung:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:160989087..160991942-chr1:161007144..161014242,6	K562	blood:
2	chr1:160989663..160992818-chr1:161011844..161017868,15	MCF-7	breast:
3	chr1:161012196..161017661-chr1:161066183..161070852,8	MCF-7	breast:
4	chr1:161012288..161019472-chr1:161047717..161055328,13	MCF-7	breast:
5	chr1:161011663..161014033-chr1:161014079..161015803,2	K562	blood:
6	chr1:160988929..160992185-chr1:161012707..161018170,8	MCF-7	breast:
7	chr1:160988071..160992174-chr1:161007125..161014242,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000270149	TF binding region
USF1	TF binding region
TSTD1	TF binding region
ENSG00000162755	Chromatin interaction
ENSG00000228917	Chromatin interaction
ENSG00000158773	Chromatin interaction
ENSG00000158769	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11576837	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap]
rs12728349	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12748157	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2073657	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2516837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2774273	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34212386	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3813609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3829791	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv947201	chr1:161006051-161013276	Weak transcription Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv3221	chr1:161008175-161052979	Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv872492	chr1:161009523-161013152	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2516839	TSTD1	cis	Artery Tibial	GTEx
rs2516839	F11R	Cis_1M	lymphoblastoid	RTeQTL
rs2516839	USF1	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161007000-161013400	Strong transcription	Cortex derived primary cultured neurospheres	brain
2	chr1:161007400-161013400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr1:161007400-161013400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr1:161007400-161013400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:161007400-161013400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:161007600-161013400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr1:161008000-161013200	Strong transcription	A549	lung
8	chr1:161008000-161013400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:161008800-161013400	Strong transcription	Brain Cingulate Gyrus	brain
10	chr1:161008800-161014000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr1:161009000-161013200	Strong transcription	Osteobl	bone
12	chr1:161009000-161013400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:161009000-161013400	Strong transcription	Fetal Stomach	stomach
14	chr1:161009000-161014000	Genic enhancers	Primary B cells from peripheral blood	blood
15	chr1:161009200-161013200	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr1:161009200-161013200	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr1:161009200-161013200	Strong transcription	Fetal Kidney	kidney
18	chr1:161009200-161013200	Strong transcription	Hela-S3	cervix
19	chr1:161009200-161013200	Strong transcription	HepG2	liver
20	chr1:161009200-161013200	Strong transcription	NH-A	brain
21	chr1:161009200-161013200	Strong transcription	NHDF-Ad	bronchial
22	chr1:161009200-161013200	Strong transcription	NHEK	skin
23	chr1:161009200-161013400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr1:161009200-161013400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
25	chr1:161009200-161013400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:161009200-161013400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr1:161009200-161013400	Strong transcription	Brain Angular Gyrus	brain
28	chr1:161009200-161013400	Strong transcription	Brain Anterior Caudate	brain
29	chr1:161009200-161013400	Strong transcription	Duodenum Smooth Muscle	Duodenum
30	chr1:161009400-161013200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr1:161009400-161013200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:161009400-161013200	Strong transcription	H9 Cell Line	embryonic stem cell
33	chr1:161009400-161013200	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr1:161009400-161013400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr1:161009400-161013400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr1:161009400-161013400	Strong transcription	HMEC	breast
37	chr1:161009400-161013400	Strong transcription	K562	blood
38	chr1:161009400-161014000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr1:161009600-161013200	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr1:161009600-161013200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr1:161009600-161013200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr1:161009600-161013200	Strong transcription	Muscle Satellite Cultured Cells	--
43	chr1:161009600-161013200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr1:161009600-161013200	Strong transcription	Fetal Intestine Large	intestine
45	chr1:161009600-161013200	Strong transcription	Fetal Intestine Small	intestine
46	chr1:161009600-161013200	Strong transcription	Gastric	stomach
47	chr1:161009600-161013200	Strong transcription	Stomach Smooth Muscle	stomach
48	chr1:161009600-161013400	Strong transcription	Fetal Muscle Trunk	muscle
49	chr1:161009600-161013400	Strong transcription	Placenta	Placenta
50	chr1:161009600-161013400	Strong transcription	HSMM	muscle

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