Variant report

Variant	rs12752953
Chromosome Location	chr1:169332170-169332171
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169331328..169334287-chr1:169334911..169337205,2	MCF-7	breast:
2	chr1:169327940..169332501-chr1:169336019..169339615,5	K562	blood:
3	chr1:169075705..169078397-chr1:169329097..169333069,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117475	Chromatin interaction
ENSG00000143156	Chromatin interaction
ENSG00000143153	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs1028180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10753786	0.82[CHB][hapmap]
rs10800447	0.81[CHB][hapmap]
rs1080268	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs10919173	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs12040141	1.00[CEU][hapmap]
rs1208373	1.00[CEU][hapmap];0.90[JPT][hapmap]
rs12121994	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12143193	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12145146	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs12145226	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12729761	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12733001	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12733037	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12733626	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12744859	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12745541	0.87[EUR][1000 genomes]
rs12748624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12751379	1.00[CEU][hapmap]
rs12751929	0.83[EUR][1000 genomes]
rs13306334	1.00[CEU][hapmap]
rs1517745	0.88[CHB][hapmap]
rs1533518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1533519	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16828165	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs16861997	1.00[CEU][hapmap]
rs16862051	1.00[CEU][hapmap]
rs16862081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16862097	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16862133	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16862153	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16862176	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16862180	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16862217	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1883167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2037249	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]
rs2066001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2203743	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2271762	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]
rs2272801	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2300158	0.82[CHB][hapmap]
rs2300160	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2420015	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2420016	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs3213586	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs3213587	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs34057682	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34373126	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34599582	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34640648	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34858340	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs34930817	0.83[EUR][1000 genomes]
rs35171152	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35406371	0.83[EUR][1000 genomes]
rs35686518	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs35918529	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36040633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3753299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3765229	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3766075	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs3766076	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs3766078	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs3766083	1.00[CEU][hapmap]
rs3766084	1.00[CEU][hapmap]
rs3766090	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3766097	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3862937	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4140538	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4140539	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs41442344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4551642	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4590731	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57295069	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58809384	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66512221	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6672589	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs6675220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs66937324	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67795749	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs724048	0.88[CHB][hapmap];0.80[JPT][hapmap]
rs72637232	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7528751	1.00[CEU][hapmap]
rs7551623	1.00[CEU][hapmap]
rs929133	0.94[CHB][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:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522071	chr1:168978325-169339044	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	esv3522072	chr1:168978325-169339044	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169270200-169336400	Weak transcription	Stomach Smooth Muscle	stomach
2	chr1:169305600-169336400	Weak transcription	Left Ventricle	heart
3	chr1:169309200-169333600	Weak transcription	Primary hematopoietic stem cells	blood
4	chr1:169309400-169336400	Weak transcription	Ovary	ovary
5	chr1:169310800-169332800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr1:169311000-169336400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:169316000-169334200	Weak transcription	Fetal Intestine Small	intestine
8	chr1:169317000-169336400	Weak transcription	Pancreas	Pancrea
9	chr1:169317200-169333800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr1:169317800-169332800	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr1:169317800-169333800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:169317800-169335800	Weak transcription	Fetal Lung	lung
13	chr1:169318000-169332200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr1:169318200-169334000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr1:169324600-169335800	Weak transcription	Primary T cells from cord blood	blood
16	chr1:169325600-169335800	Weak transcription	K562	blood
17	chr1:169326200-169334200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr1:169327200-169335800	Weak transcription	Small Intestine	intestine
19	chr1:169327200-169336200	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr1:169328400-169332800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr1:169329800-169332200	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr1:169330000-169332600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:169330000-169336400	Weak transcription	Psoas Muscle	Psoas
24	chr1:169330200-169332800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:169330800-169335800	Weak transcription	Brain Hippocampus Middle	brain
26	chr1:169330800-169336400	Weak transcription	Right Ventricle	heart
27	chr1:169331000-169332600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:169331400-169335800	Weak transcription	Fetal Intestine Large	intestine
29	chr1:169331600-169333200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr1:169331600-169333400	Enhancers	Osteobl	bone
31	chr1:169331600-169335600	Enhancers	HMEC	breast
32	chr1:169331800-169332800	Enhancers	Hela-S3	cervix
33	chr1:169331800-169332800	Enhancers	NH-A	brain
34	chr1:169331800-169333000	Enhancers	Placenta Amnion	Placenta Amnion
35	chr1:169331800-169333000	Enhancers	NHDF-Ad	bronchial
36	chr1:169331800-169333200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr1:169331800-169333400	Enhancers	Muscle Satellite Cultured Cells	--
38	chr1:169331800-169333400	Enhancers	HUVEC	blood vessel
39	chr1:169331800-169333600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr1:169331800-169335800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr1:169331800-169336200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr1:169332000-169332200	Weak transcription	HSMM	muscle
43	chr1:169332000-169332400	Weak transcription	NHLF	lung
44	chr1:169332000-169332600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr1:169332000-169332600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr1:169332000-169332600	Enhancers	GM12878-XiMat	blood
47	chr1:169332000-169333600	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr1:169332000-169334400	Enhancers	NHEK	skin
49	chr1:169332000-169335800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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