Variant report

Variant	rs3772692
Chromosome Location	chr3:100104058-100104059
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:5)
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	GATA3	chr3:100104000-100104138	SH-SY5Y	brain:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:100102691..100105563-chr3:100122980..100125104,2	MCF-7	breast:
2	chr3:100097916..100106101-chr3:100115627..100122137,10	K562	blood:
3	chr3:100102836..100105510-chr3:100118455..100121346,2	K562	blood:
4	chr3:100098158..100099923-chr3:100101288..100104122,2	K562	blood:
5	chr3:100099778..100102501-chr3:100103098..100105700,3	K562	blood:

No data

Variant related genes	Relation type
TOMM70A	TF binding region
ENSG00000206535	Chromatin interaction
ENSG00000154174	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10936180	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1123578	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1214380	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1214381	1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1228184	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12495001	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1530283	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs166747	1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs277620	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs277622	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs277623	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs277626	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs277628	0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs277629	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs277630	0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs277633	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277634	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs277635	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277638	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs277639	0.91[MEX][hapmap]
rs277641	0.91[MEX][hapmap]
rs277642	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277644	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277651	0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs372438	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3806615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs392066	0.85[GIH][hapmap];0.82[MEX][hapmap];0.84[AMR][1000 genomes]
rs402870	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs413425	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs431069	0.95[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs432715	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6780662	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.93[YRI][hapmap];0.92[ASN][1000 genomes]
rs6791102	0.92[ASN][1000 genomes]
rs6794955	0.85[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7616634	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7641630	0.86[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.93[YRI][hapmap];0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]

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	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1003924	chr3:99933762-100112690	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100071000-100104400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr3:100071400-100105800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr3:100077000-100106000	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr3:100077200-100105600	Strong transcription	Duodenum Mucosa	Duodenum
5	chr3:100077600-100105200	Strong transcription	Skeletal Muscle Female	skeletal muscle
6	chr3:100078800-100104400	Strong transcription	Fetal Intestine Large	intestine
7	chr3:100079400-100107600	Strong transcription	Dnd41	blood
8	chr3:100079600-100106200	Strong transcription	Primary B cells from peripheral blood	blood
9	chr3:100079800-100106200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr3:100080200-100104400	Strong transcription	Duodenum Smooth Muscle	Duodenum
11	chr3:100080200-100106200	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr3:100080600-100105800	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr3:100081000-100106000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr3:100081200-100104800	Strong transcription	Adipose Nuclei	Adipose
15	chr3:100081200-100105200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr3:100081200-100106000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr3:100081200-100106200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr3:100081200-100107000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:100081200-100107000	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr3:100081200-100107800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:100081400-100106200	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr3:100081800-100104200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:100081800-100106200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:100082200-100107200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr3:100082400-100105800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr3:100083000-100106000	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr3:100083400-100105200	Strong transcription	Placenta	Placenta
28	chr3:100084800-100105600	Weak transcription	Fetal Heart	heart
29	chr3:100087600-100114600	Weak transcription	Small Intestine	intestine
30	chr3:100089000-100104200	Strong transcription	Primary T cells from cord blood	blood
31	chr3:100089000-100104600	Strong transcription	A549	lung
32	chr3:100089000-100104800	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr3:100089000-100105800	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr3:100089000-100106000	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr3:100089000-100106000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr3:100089200-100104400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr3:100089200-100107200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr3:100089400-100105400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr3:100090000-100105800	Strong transcription	Primary hematopoietic stem cells	blood
40	chr3:100090200-100118400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr3:100091600-100117600	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr3:100093200-100106400	Strong transcription	GM12878-XiMat	blood
43	chr3:100093600-100105800	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr3:100093800-100104200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr3:100093800-100105200	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr3:100094000-100106000	Weak transcription	Ovary	ovary
47	chr3:100094400-100105400	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr3:100094400-100106000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr3:100094600-100104600	Strong transcription	Fetal Thymus	thymus
50	chr3:100094600-100105400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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