Variant report

Variant	rs9942075
Chromosome Location	chr3:141722878-141722879
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr3:141722809-141723298	T-47D	breast:	n/a	n/a
2	GATA3	chr3:141722704-141723419	SK-N-SH	brain:	n/a	n/a
3	FOXA1	chr3:141722873-141723176	T-47D	breast:	n/a	n/a
4	GATA3	chr3:141722818-141723244	T-47D	breast:	n/a	n/a
5	EP300	chr3:141722697-141723368	T-47D	breast:	n/a	n/a

Variant related genes	Relation type
TFDP2	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10935453	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11706480	0.90[CEU][hapmap];0.94[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11714792	0.86[EUR][1000 genomes]
rs12496412	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13065446	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1355438	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs1397764	0.94[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs1511299	0.85[ASN][1000 genomes]
rs2861422	0.94[CHB][hapmap];0.82[CHD][hapmap];0.88[JPT][hapmap];0.82[MEX][hapmap];0.86[ASN][1000 genomes]
rs2862125	0.81[ASN][1000 genomes]
rs34186890	0.86[ASN][1000 genomes]
rs34392664	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35566385	0.87[EUR][1000 genomes]
rs4683653	0.82[ASW][hapmap];0.90[TSI][hapmap]
rs4683658	0.81[ASN][1000 genomes]
rs6440057	0.83[ASN][1000 genomes]
rs6773343	0.82[JPT][hapmap]
rs6781340	0.90[CEU][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6791514	0.89[CHB][hapmap];0.88[JPT][hapmap]
rs6794342	0.92[EUR][1000 genomes]
rs7630893	0.80[ASN][1000 genomes]
rs7642874	0.81[CEU][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes]
rs7644155	0.81[ASN][1000 genomes]
rs7644383	0.88[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs9848817	1.00[CEU][hapmap];0.94[CHB][hapmap];0.88[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9877536	0.90[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[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	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1013352	chr3:141541105-141870293	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv1002446	chr3:141719169-142070290	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141629000-141739200	Weak transcription	Psoas Muscle	Psoas
2	chr3:141671800-141724000	Weak transcription	Right Ventricle	heart
3	chr3:141671800-141735600	Weak transcription	Aorta	Aorta
4	chr3:141677800-141739000	Weak transcription	Left Ventricle	heart
5	chr3:141678800-141745600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr3:141680000-141731200	Weak transcription	Fetal Brain Female	brain
7	chr3:141680800-141723200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr3:141682600-141723400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr3:141682800-141724600	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr3:141682800-141739000	Weak transcription	Pancreas	Pancrea
11	chr3:141682800-141745800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr3:141682800-141746200	Weak transcription	Primary B cells from peripheral blood	blood
13	chr3:141683800-141746600	Weak transcription	Lung	lung
14	chr3:141688800-141729000	Strong transcription	Fetal Thymus	thymus
15	chr3:141697400-141727200	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr3:141697600-141725800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr3:141698600-141738800	Weak transcription	HSMM	muscle
18	chr3:141704200-141725400	Weak transcription	Spleen	Spleen
19	chr3:141706400-141746200	Weak transcription	Fetal Lung	lung
20	chr3:141707200-141734400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:141708400-141731200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:141708600-141728400	Weak transcription	Liver	Liver
23	chr3:141708600-141745200	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr3:141711800-141732400	Weak transcription	Stomach Smooth Muscle	stomach
25	chr3:141713000-141724400	Weak transcription	Duodenum Mucosa	Duodenum
26	chr3:141715800-141723200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr3:141716000-141723000	Weak transcription	HSMMtube	muscle
28	chr3:141716000-141724600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:141716000-141732400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr3:141716000-141738600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:141716000-141745600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr3:141716600-141724000	Weak transcription	Ovary	ovary
33	chr3:141718600-141724200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr3:141719000-141724200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr3:141719600-141723000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:141719600-141724600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:141719600-141738600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr3:141719600-141738600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr3:141719600-141739000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr3:141719800-141728600	Strong transcription	Dnd41	blood
41	chr3:141720000-141724400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr3:141720200-141725800	Weak transcription	Fetal Muscle Trunk	muscle
43	chr3:141720200-141738000	Weak transcription	Fetal Intestine Large	intestine
44	chr3:141720200-141746600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr3:141720400-141732400	Weak transcription	Fetal Stomach	stomach
46	chr3:141720400-141737400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr3:141720400-141742600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr3:141720600-141730000	Weak transcription	Primary T cells from cord blood	blood
49	chr3:141721200-141724600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr3:141721200-141725400	Weak transcription	Fetal Intestine Small	intestine

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