Variant report

Variant	rs17475431
Chromosome Location	chr1:222989700-222989701
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:222986729..222989819-chr1:223001002..223005734,5	MCF-7	breast:
2	chr1:222988355..222990367-chr1:223003630..223006609,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000228106	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10495202	0.94[EUR][1000 genomes]
rs1132369	0.94[EUR][1000 genomes]
rs1132371	0.94[EUR][1000 genomes]
rs17475753	0.94[EUR][1000 genomes]
rs17475774	0.94[EUR][1000 genomes]
rs17534704	0.94[EUR][1000 genomes]
rs17534774	0.95[EUR][1000 genomes]
rs17535004	0.94[EUR][1000 genomes]
rs17535032	0.96[EUR][1000 genomes]
rs17535137	0.94[EUR][1000 genomes]
rs2378600	1.00[AFR][1000 genomes]
rs28362013	1.00[ASN][1000 genomes]
rs34096996	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34139393	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34151467	0.94[EUR][1000 genomes]
rs34225287	0.94[EUR][1000 genomes]
rs34229647	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34277924	0.94[EUR][1000 genomes]
rs34282641	1.00[AFR][1000 genomes]
rs34299243	0.94[EUR][1000 genomes]
rs34300028	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34505570	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34651530	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs34690779	0.94[EUR][1000 genomes]
rs34713681	0.94[EUR][1000 genomes]
rs34755094	0.94[EUR][1000 genomes]
rs34761499	0.94[EUR][1000 genomes]
rs34791822	0.94[EUR][1000 genomes]
rs34804073	0.94[EUR][1000 genomes]
rs34830798	1.00[AFR][1000 genomes]
rs34893395	0.94[EUR][1000 genomes]
rs34898792	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34950986	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35131473	0.94[EUR][1000 genomes]
rs35197173	0.96[EUR][1000 genomes]
rs35270311	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35270996	0.87[EUR][1000 genomes]
rs35283922	0.94[EUR][1000 genomes]
rs35356885	0.94[EUR][1000 genomes]
rs35399857	0.94[EUR][1000 genomes]
rs35497286	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35591569	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35756512	0.94[EUR][1000 genomes]
rs35787799	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs36032255	0.94[EUR][1000 genomes]
rs36066427	0.94[EUR][1000 genomes]
rs36083483	1.00[ASN][1000 genomes]
rs36090356	0.93[EUR][1000 genomes]
rs4609435	1.00[ASN][1000 genomes]
rs61838099	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61838105	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61838107	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61838112	1.00[ASN][1000 genomes]
rs61838113	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61838114	1.00[ASN][1000 genomes]
rs61838115	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61838118	0.94[EUR][1000 genomes]
rs61838119	0.94[EUR][1000 genomes]
rs61839587	0.94[EUR][1000 genomes]
rs61839588	0.94[EUR][1000 genomes]
rs61839600	0.94[EUR][1000 genomes]
rs61839601	0.93[EUR][1000 genomes]
rs61839602	0.93[EUR][1000 genomes]
rs71644708	0.94[EUR][1000 genomes]

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	nsv999185	chr1:222500725-223278032	Strong transcription Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
2	nsv535304	chr1:222500725-223278032	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
4	nsv873206	chr1:222985197-223124916	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:222987800-222990000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr1:222988000-222989800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr1:222988200-222989800	Active TSS	Muscle Satellite Cultured Cells	--
4	chr1:222989000-222990000	Flanking Active TSS	Dnd41	blood
5	chr1:222989000-222990800	Weak transcription	Small Intestine	intestine
6	chr1:222989000-222999200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:222989200-222989800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr1:222989200-222989800	Enhancers	Primary B cells from cord blood	blood
9	chr1:222989200-222989800	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr1:222989200-222990000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr1:222989200-222990200	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr1:222989200-222990200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr1:222989200-222990200	Weak transcription	HSMM	muscle
14	chr1:222989200-222990600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr1:222989200-222990800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:222989200-222990800	Weak transcription	Primary B cells from peripheral blood	blood
17	chr1:222989200-222990800	Weak transcription	Aorta	Aorta
18	chr1:222989200-222991000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr1:222989200-222991000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:222989200-222991400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr1:222989200-222991400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr1:222989200-222992400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:222989200-222992400	Weak transcription	Ovary	ovary
24	chr1:222989200-222992400	Enhancers	Rectal Smooth Muscle	rectum
25	chr1:222989200-222993000	Weak transcription	Fetal Thymus	thymus
26	chr1:222989200-222994000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr1:222989200-222997600	Weak transcription	Fetal Brain Male	brain
28	chr1:222989200-222999000	Weak transcription	Lung	lung
29	chr1:222989400-222989800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr1:222989400-222989800	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr1:222989400-222989800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
32	chr1:222989400-222989800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr1:222989400-222989800	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr1:222989400-222989800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr1:222989400-222989800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:222989400-222989800	Enhancers	Fetal Stomach	stomach
37	chr1:222989400-222989800	Enhancers	Stomach Smooth Muscle	stomach
38	chr1:222989400-222990000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr1:222989400-222990000	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr1:222989400-222990000	Enhancers	Liver	Liver
41	chr1:222989400-222990000	Enhancers	Brain Germinal Matrix	brain
42	chr1:222989400-222990000	Enhancers	Duodenum Mucosa	Duodenum
43	chr1:222989400-222990000	Enhancers	NHEK	skin
44	chr1:222989400-222990200	Weak transcription	Psoas Muscle	Psoas
45	chr1:222989400-222990200	Weak transcription	HSMMtube	muscle
46	chr1:222989400-222990600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr1:222989400-222990600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr1:222989400-222990600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:222989400-222990600	Weak transcription	GM12878-XiMat	blood
50	chr1:222989400-222990600	Weak transcription	HMEC	breast

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