Variant report

Variant	rs2271762
Chromosome Location	chr1:169347545-169347546
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169347200..169349790-chr1:169495385..169498063,2	MCF-7	breast:
2	chr1:169338197..169339910-chr1:169345261..169347920,2	MCF-7	breast:
3	chr1:169346482..169351680-chr1:169353078..169360345,13	K562	blood:
4	chr1:169341801..169344771-chr1:169346777..169350780,3	MCF-7	breast:
5	chr1:169346112..169350144-chr1:169384504..169386593,3	K562	blood:

Extended variants
information (count: 110 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs1028180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753786	0.83[CHB][hapmap]
rs10800447	0.83[CHB][hapmap]
rs1080268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10919173	0.89[CHB][hapmap]
rs12040141	1.00[CEU][hapmap]
rs1208373	1.00[CEU][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs12121994	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs12143193	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12145146	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12145226	1.00[CHB][hapmap];1.00[JPT][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[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs12733037	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12733626	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12735250	0.82[EUR][1000 genomes]
rs12743782	0.82[EUR][1000 genomes]
rs12744859	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12745541	0.91[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12748624	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs12751379	1.00[CEU][hapmap]
rs12752953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs1517745	0.89[CHB][hapmap]
rs1533518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1533519	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]
rs16828165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16861997	1.00[CEU][hapmap]
rs16862051	1.00[CEU][hapmap]
rs16862081	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs16862097	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[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[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16862217	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1883167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2037249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2066001	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][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]
rs2272801	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2300158	0.83[CHB][hapmap]
rs2300160	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2420015	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2420016	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3213586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs3213587	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs36179730	0.82[EUR][1000 genomes]
rs3753299	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs3765229	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3766075	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3766076	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs3766078	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3766083	1.00[CEU][hapmap]
rs3766084	1.00[CEU][hapmap]
rs3766090	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs3766097	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3862937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4140538	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs4140539	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes]
rs41442344	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][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]
rs6672589	0.89[CHB][hapmap]
rs6675220	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][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	0.88[CHB][hapmap];0.85[JPT][hapmap];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]
rs929133	0.94[CHB][hapmap];0.81[CHD][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:5 , 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	nsv1010010	chr1:169189586-169347545	Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription 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	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
4	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
5	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2271762	FOXQ1	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169338000-169351200	Weak transcription	Lung	lung
2	chr1:169338000-169351200	Weak transcription	Spleen	Spleen
3	chr1:169338000-169353600	Weak transcription	Small Intestine	intestine
4	chr1:169338000-169358000	Weak transcription	Esophagus	oesophagus
5	chr1:169338000-169360000	Weak transcription	Fetal Heart	heart
6	chr1:169338000-169360400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:169338000-169365200	Weak transcription	Gastric	stomach
8	chr1:169338000-169365600	Weak transcription	Pancreas	Pancrea
9	chr1:169338200-169351800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr1:169338200-169360400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:169338200-169360400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:169338200-169362200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:169338200-169363600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr1:169338200-169363600	Weak transcription	Stomach Mucosa	stomach
15	chr1:169338200-169369000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr1:169338400-169349600	Weak transcription	HSMMtube	muscle
17	chr1:169338400-169360200	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr1:169338400-169362600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:169338600-169349800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr1:169338600-169351400	Weak transcription	Thymus	Thymus
21	chr1:169338600-169352200	Weak transcription	Aorta	Aorta
22	chr1:169338600-169352200	Weak transcription	Fetal Stomach	stomach
23	chr1:169338600-169352400	Weak transcription	Fetal Intestine Small	intestine
24	chr1:169338600-169352800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr1:169338600-169357600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr1:169339200-169351800	Weak transcription	Fetal Brain Male	brain
27	chr1:169339400-169347600	Weak transcription	Rectal Smooth Muscle	rectum
28	chr1:169339600-169351000	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr1:169340200-169356400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:169340400-169366000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:169341000-169351400	Weak transcription	Brain Hippocampus Middle	brain
32	chr1:169341200-169349600	Weak transcription	GM12878-XiMat	blood
33	chr1:169341200-169367400	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr1:169342800-169351200	Weak transcription	Fetal Muscle Leg	muscle
35	chr1:169343000-169347600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr1:169343000-169351400	Weak transcription	K562	blood
37	chr1:169344200-169360200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:169344600-169348000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr1:169344800-169348600	Strong transcription	Adipose Nuclei	Adipose
40	chr1:169344800-169359200	Strong transcription	HSMM	muscle
41	chr1:169344800-169361200	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr1:169344800-169362600	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr1:169344800-169365400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr1:169345000-169355400	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr1:169345000-169360800	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr1:169345000-169366000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:169345200-169348200	Strong transcription	Liver	Liver
48	chr1:169345200-169348400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr1:169345200-169348600	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr1:169345200-169348600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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