Variant report

Variant	rs17557525
Chromosome Location	chr1:223907298-223907299
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:223907255..223908800-chr1:223930400..223932243,2	MCF-7	breast:
2	chr1:223906912..223908483-chr1:223923323..223925771,2	MCF-7	breast:
3	chr1:223906267..223909049-chr1:223925924..223927616,2	MCF-7	breast:
4	chr1:223885961..223896993-chr1:223898177..223910405,32	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162909	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10465524	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs10495215	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.85[MEX][hapmap];0.81[MKK][hapmap];0.82[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10495216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10495217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10503144	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs10915702	0.81[EUR][1000 genomes]
rs12059770	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12066704	0.85[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs12066829	0.81[EUR][1000 genomes]
rs12066831	0.81[EUR][1000 genomes]
rs12069561	0.85[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap]
rs12070057	0.81[EUR][1000 genomes]
rs12080250	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs12088254	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap]
rs1222138	0.85[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs1222140	0.84[EUR][1000 genomes]
rs1222141	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs1222142	0.83[EUR][1000 genomes]
rs12563291	0.83[EUR][1000 genomes]
rs12563637	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs12563713	0.82[EUR][1000 genomes]
rs12565967	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12566817	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs12568612	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1629836	1.00[CEU][hapmap]
rs16841190	1.00[JPT][hapmap]
rs16842162	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs16842257	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs16842326	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs16842343	1.00[JPT][hapmap]
rs17556570	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs17557288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17557623	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17597	0.83[EUR][1000 genomes]
rs17598	0.85[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap]
rs28370026	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28370031	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28370032	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28370043	0.99[EUR][1000 genomes]
rs3738373	0.85[CEU][hapmap];0.88[TSI][hapmap]
rs3738374	0.85[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap]
rs4653522	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4993742	0.82[CEU][hapmap]
rs59248553	0.81[EUR][1000 genomes]
rs59275322	0.84[EUR][1000 genomes]
rs61823964	0.83[EUR][1000 genomes]
rs61823979	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604724	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6671245	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6678365	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs6683052	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6685475	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6685557	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6691315	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6693372	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6693884	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6694960	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6696053	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6700366	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap]
rs6703104	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7331	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs751609	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs7530328	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7533551	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7535882	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs7549063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7555226	0.84[EUR][1000 genomes]
rs898876	0.81[EUR][1000 genomes]
rs898877	0.80[EUR][1000 genomes]

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	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
5	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv873213	chr1:223885843-223924236	Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	20 gene(s)	inside rSNPs	diseases
7	nsv1008800	chr1:223904653-224061032	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223901400-223907600	Transcr. at gene 5' and 3'	A549	lung
2	chr1:223902200-223913400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:223902800-223914200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:223903000-223907800	Weak transcription	Liver	Liver
5	chr1:223903200-223913600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:223903400-223907400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
7	chr1:223903400-223908400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:223903400-223908800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:223903600-223909400	Strong transcription	Cortex derived primary cultured neurospheres	brain
10	chr1:223903600-223911800	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:223903600-223922400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:223904000-223909000	Genic enhancers	Hela-S3	cervix
13	chr1:223904000-223910000	Genic enhancers	Osteobl	bone
14	chr1:223904200-223909800	Genic enhancers	NH-A	brain
15	chr1:223904400-223907400	Genic enhancers	HMEC	breast
16	chr1:223904400-223910000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:223904400-223913000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:223904400-223922400	Genic enhancers	NHLF	lung
19	chr1:223904600-223907600	Weak transcription	Small Intestine	intestine
20	chr1:223904600-223908000	Weak transcription	Thymus	Thymus
21	chr1:223904600-223908600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr1:223904600-223908600	Weak transcription	Right Atrium	heart
23	chr1:223904600-223909800	Genic enhancers	HUVEC	blood vessel
24	chr1:223904600-223913600	Strong transcription	Brain Anterior Caudate	brain
25	chr1:223904600-223914000	Genic enhancers	NHDF-Ad	bronchial
26	chr1:223904800-223907400	Strong transcription	K562	blood
27	chr1:223904800-223908000	Genic enhancers	Placenta	Placenta
28	chr1:223904800-223908400	Strong transcription	Skeletal Muscle Male	skeletal muscle
29	chr1:223904800-223909000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:223904800-223909000	Strong transcription	Brain Angular Gyrus	brain
31	chr1:223904800-223909200	Strong transcription	Brain Cingulate Gyrus	brain
32	chr1:223904800-223909400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr1:223904800-223909400	Strong transcription	Brain Inferior Temporal Lobe	brain
34	chr1:223904800-223909600	Genic enhancers	HSMM	muscle
35	chr1:223904800-223910600	Genic enhancers	Muscle Satellite Cultured Cells	--
36	chr1:223904800-223911800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:223904800-223913200	Strong transcription	Fetal Stomach	stomach
38	chr1:223904800-223914000	Genic enhancers	Primary T cells fromperipheralblood	blood
39	chr1:223905000-223907400	Genic enhancers	Rectal Mucosa Donor 31	rectum
40	chr1:223905000-223908400	Strong transcription	Brain Substantia Nigra	brain
41	chr1:223905000-223908400	Strong transcription	Colon Smooth Muscle	Colon
42	chr1:223905000-223909200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr1:223905000-223911600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr1:223905200-223908000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr1:223905200-223908400	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr1:223905200-223908400	Strong transcription	Stomach Smooth Muscle	stomach
47	chr1:223905200-223908600	Strong transcription	Left Ventricle	heart
48	chr1:223905200-223909000	Strong transcription	Esophagus	oesophagus
49	chr1:223905200-223909400	Strong transcription	Brain Germinal Matrix	brain
50	chr1:223905200-223911400	Strong transcription	Fetal Muscle Leg	muscle

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