Variant report

Variant	rs1533519
Chromosome Location	chr1:169351992-169351993
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	chr1:169345044..169346763-chr1:169350372..169352525,2	MCF-7	breast:
2	chr1:169351714..169354510-chr1:169454389..169456907,2	K562	blood:

Variant related genes	Relation type
ENSG00000213062	Chromatin interaction
ENSG00000117479	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs1028180	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1080268	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs12040141	1.00[CEU][hapmap]
rs1208373	1.00[CEU][hapmap]
rs12725912	0.82[EUR][1000 genomes]
rs12727318	0.80[AMR][1000 genomes]
rs12729761	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs12733001	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs12733037	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12735250	0.82[EUR][1000 genomes]
rs12743782	0.82[EUR][1000 genomes]
rs12744859	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12745541	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12748624	1.00[CEU][hapmap]
rs12751379	1.00[CEU][hapmap]
rs12752953	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12757669	0.82[EUR][1000 genomes]
rs13306334	1.00[CEU][hapmap]
rs1533518	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16828165	1.00[CEU][hapmap]
rs16861997	1.00[CEU][hapmap]
rs16862051	1.00[CEU][hapmap]
rs16862081	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs16862097	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16862133	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16862153	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16862176	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16862180	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16862217	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1883167	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2037249	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066001	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs2203743	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2271762	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2272801	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3213586	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs3213587	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs34057682	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34373126	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34599582	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34640648	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34689938	0.82[EUR][1000 genomes]
rs34848249	0.82[EUR][1000 genomes]
rs34858340	0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs34989506	0.80[AMR][1000 genomes]
rs35171152	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35244822	0.82[EUR][1000 genomes]
rs35435858	0.82[EUR][1000 genomes]
rs35448601	0.82[EUR][1000 genomes]
rs35493809	0.82[EUR][1000 genomes]
rs35639586	0.82[EUR][1000 genomes]
rs35653716	0.82[EUR][1000 genomes]
rs35680826	0.82[EUR][1000 genomes]
rs35686518	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs35918529	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36023090	0.82[EUR][1000 genomes]
rs36040633	1.00[CEU][hapmap]
rs36179730	0.82[EUR][1000 genomes]
rs3753299	1.00[CEU][hapmap]
rs3765229	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3766075	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs3766076	1.00[YRI][hapmap]
rs3766083	1.00[CEU][hapmap]
rs3766084	1.00[CEU][hapmap]
rs3766097	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3862937	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4140538	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs4140539	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs41442344	1.00[CEU][hapmap]
rs4551642	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4590731	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57295069	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58809384	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66512221	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6675220	1.00[CEU][hapmap]
rs66937324	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67795749	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71635619	0.82[EUR][1000 genomes]
rs724048	1.00[YRI][hapmap]
rs72637232	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7528751	1.00[CEU][hapmap]
rs7551623	1.00[CEU][hapmap]
rs9332623	1.00[CEU][hapmap]
rs9332624	1.00[CEU][hapmap]
rs9332628	1.00[CEU][hapmap]
rs9332647	1.00[CEU][hapmap]
rs9332658	1.00[CEU][hapmap]
rs9332678	1.00[CEU][hapmap]

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	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv872531	chr1:169191860-169388193	Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv872532	chr1:169275630-169363203	Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv831871	chr1:169320673-169486680	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169338000-169353600	Weak transcription	Small Intestine	intestine
2	chr1:169338000-169358000	Weak transcription	Esophagus	oesophagus
3	chr1:169338000-169360000	Weak transcription	Fetal Heart	heart
4	chr1:169338000-169360400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:169338000-169365200	Weak transcription	Gastric	stomach
6	chr1:169338000-169365600	Weak transcription	Pancreas	Pancrea
7	chr1:169338200-169360400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:169338200-169360400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:169338200-169362200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:169338200-169363600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr1:169338200-169363600	Weak transcription	Stomach Mucosa	stomach
12	chr1:169338200-169369000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:169338400-169360200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr1:169338400-169362600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:169338600-169352200	Weak transcription	Aorta	Aorta
16	chr1:169338600-169352200	Weak transcription	Fetal Stomach	stomach
17	chr1:169338600-169352400	Weak transcription	Fetal Intestine Small	intestine
18	chr1:169338600-169352800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr1:169338600-169357600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:169340200-169356400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:169340400-169366000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:169341200-169367400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr1:169344200-169360200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:169344800-169359200	Strong transcription	HSMM	muscle
25	chr1:169344800-169361200	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr1:169344800-169362600	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr1:169344800-169365400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr1:169345000-169355400	Strong transcription	Rectal Mucosa Donor 31	rectum
29	chr1:169345000-169360800	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr1:169345000-169366000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:169345200-169352200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:169345200-169352400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr1:169345200-169353600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:169345400-169353600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:169345400-169354000	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr1:169345400-169366000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
37	chr1:169345600-169352400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr1:169345600-169352800	Strong transcription	HUVEC	blood vessel
39	chr1:169345600-169355000	Strong transcription	A549	lung
40	chr1:169345600-169360800	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr1:169345600-169366000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr1:169345800-169354200	Strong transcription	NHDF-Ad	bronchial
43	chr1:169345800-169360800	Strong transcription	NH-A	brain
44	chr1:169345800-169365000	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr1:169345800-169365400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr1:169345800-169366000	Strong transcription	Placenta	Placenta
47	chr1:169345800-169366400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr1:169346600-169354800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr1:169346600-169363400	Weak transcription	Right Ventricle	heart
50	chr1:169346600-169365400	Weak transcription	HepG2	liver

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