Variant report

Variant	rs2050619
Chromosome Location	chr1:165640925-165640926
allele	C/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	MYC	chr1:165640804-165641099	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr1:165640766-165641171	MCF10A-Er-Src	breast:	n/a	n/a
3	STAT3	chr1:165640840-165641099	MCF10A-Er-Src	breast:	n/a	chr1:165640983-165640991
4	POLR2A	chr1:165640877-165641098	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr1:165640839-165641180	MCF10A-Er-Src	breast:	n/a	chr1:165640983-165640991
6	MYC	chr1:165640860-165641171	MCF10A-Er-Src	breast:	n/a	n/a
7	E2F4	chr1:165640814-165641190	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr1:165640765-165641170	MCF10A-Er-Src	breast:	n/a	n/a
9	STAT3	chr1:165640722-165641256	MCF10A-Er-Src	breast:	n/a	chr1:165640983-165640991
10	CEBPB	chr1:165640895-165641153	A549	lung:	n/a	chr1:165640996-165641009
11	STAT3	chr1:165640775-165641100	MCF10A-Er-Src	breast:	n/a	chr1:165640983-165640991
12	FOS	chr1:165640760-165641144	MCF10A-Er-Src	breast:	n/a	n/a
13	FOS	chr1:165640776-165641108	MCF10A-Er-Src	breast:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MGST3-3	chr1:165640493-165640962	NONHSAT007330

Variant related genes	Relation type
ENSG00000225272	TF binding region

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10157944	0.81[ASN][1000 genomes]
rs10494446	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10494447	0.87[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10800122	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10800123	0.87[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10800125	0.83[CHB][hapmap]
rs10800126	0.91[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10918229	0.87[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10918230	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10918231	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10918235	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10918238	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10918239	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10918240	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12065621	0.83[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs12069198	0.81[ASN][1000 genomes]
rs12072634	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs12072664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12080699	0.83[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs12081903	0.83[CHB][hapmap]
rs12083091	0.81[ASN][1000 genomes]
rs12083232	0.81[ASN][1000 genomes]
rs12123278	0.84[ASN][1000 genomes]
rs12670	1.00[ASW][hapmap];0.91[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.87[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17417191	0.81[ASN][1000 genomes]
rs17450889	0.81[ASN][1000 genomes]
rs1878074	0.87[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1878075	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2176151	0.84[ASN][1000 genomes]
rs2184918	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2297762	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2297763	0.83[CHB][hapmap]
rs2297765	0.92[CHB][hapmap]
rs2348727	0.83[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs2348728	0.83[CHB][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs2348729	0.84[ASN][1000 genomes]
rs3795540	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3820362	0.83[CHB][hapmap]
rs4147603	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4147604	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4147605	0.87[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4147606	0.87[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4147607	0.83[ASN][1000 genomes]
rs4147608	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4147609	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4147610	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4147611	0.87[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4427389	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4539111	0.91[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4581256	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4590653	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4638106	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4646895	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs4646896	0.81[ASN][1000 genomes]
rs4646897	0.82[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs61800420	0.81[ASN][1000 genomes]
rs61800421	0.81[ASN][1000 genomes]
rs6657651	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6662419	0.81[ASN][1000 genomes]
rs6667075	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6669697	0.81[ASN][1000 genomes]
rs6683651	0.81[ASN][1000 genomes]
rs6683665	0.81[ASN][1000 genomes]
rs6683969	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs7534437	0.92[CHB][hapmap];0.81[ASN][1000 genomes]
rs8133	0.83[CHB][hapmap]
rs884121	0.89[ASN][1000 genomes]
rs9333483	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9333489	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9333490	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9333494	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9333496	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv946481	chr1:165639060-165646269	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 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	chr1:165606200-165659600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:165618200-165652400	Strong transcription	Fetal Muscle Leg	muscle
3	chr1:165619000-165642600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr1:165619000-165643600	Strong transcription	Fetal Muscle Trunk	muscle
5	chr1:165619200-165648800	Strong transcription	Liver	Liver
6	chr1:165619600-165642600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:165619600-165653200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr1:165623400-165653000	Weak transcription	Stomach Mucosa	stomach
9	chr1:165628000-165646600	Strong transcription	Primary T cells from cord blood	blood
10	chr1:165628800-165642000	Strong transcription	HSMM	muscle
11	chr1:165628800-165642200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:165628800-165644000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:165628800-165646800	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr1:165628800-165646800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr1:165629000-165653600	Strong transcription	Dnd41	blood
16	chr1:165629200-165641600	Strong transcription	Duodenum Mucosa	Duodenum
17	chr1:165629200-165642800	Strong transcription	Primary hematopoietic stem cells	blood
18	chr1:165629200-165643600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:165629400-165642200	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr1:165629400-165642600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:165629400-165652800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr1:165629400-165654200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr1:165629400-165656000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:165629600-165641800	Strong transcription	Fetal Lung	lung
25	chr1:165629600-165643000	Strong transcription	Primary B cells from cord blood	blood
26	chr1:165629600-165654800	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr1:165629800-165642000	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr1:165629800-165643600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:165629800-165654800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr1:165630000-165642200	Strong transcription	Fetal Thymus	thymus
31	chr1:165630000-165642200	Strong transcription	Thymus	Thymus
32	chr1:165630000-165654400	Strong transcription	Primary B cells from peripheral blood	blood
33	chr1:165631000-165643400	Strong transcription	Hela-S3	cervix
34	chr1:165632200-165645400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr1:165632400-165649400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr1:165633600-165651200	Weak transcription	Pancreas	Pancrea
37	chr1:165633600-165651400	Weak transcription	Gastric	stomach
38	chr1:165633800-165651000	Weak transcription	Small Intestine	intestine
39	chr1:165634400-165644600	Weak transcription	Fetal Brain Male	brain
40	chr1:165634400-165651800	Weak transcription	Fetal Heart	heart
41	chr1:165634600-165644800	Weak transcription	Brain Hippocampus Middle	brain
42	chr1:165635200-165647800	Weak transcription	Brain Cingulate Gyrus	brain
43	chr1:165635800-165645600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr1:165635800-165648600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr1:165636000-165652400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr1:165636200-165642000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr1:165636400-165643600	Strong transcription	Fetal Intestine Small	intestine
48	chr1:165636600-165641000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:165636600-165642600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr1:165637800-165645400	Weak transcription	Right Ventricle	heart

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