Variant report

Variant	rs17112402
Chromosome Location	chr1:56044914-56044915
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ESR1	chr1:56044890-56045264	ECC-1	luminal epithelium:	n/a	n/a

Variant related genes	Relation type
ENSG00000234810	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10493196	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10749702	0.81[CEU][hapmap]
rs10789002	0.85[EUR][1000 genomes]
rs10789003	0.85[EUR][1000 genomes]
rs10789004	0.85[EUR][1000 genomes]
rs10888933	0.83[EUR][1000 genomes]
rs10888934	0.85[EUR][1000 genomes]
rs11206620	0.84[EUR][1000 genomes]
rs11206622	0.85[EUR][1000 genomes]
rs11206625	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11206629	0.85[CEU][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11206636	0.81[CEU][hapmap];0.81[AMR][1000 genomes]
rs11206637	0.81[AMR][1000 genomes]
rs11206638	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11807964	0.83[CEU][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12026971	0.81[CEU][hapmap];0.84[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12040862	0.84[CEU][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12041985	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs12086546	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12128337	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12132336	0.81[CEU][hapmap];0.81[AMR][1000 genomes]
rs12139752	0.81[AMR][1000 genomes]
rs12142554	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12401977	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1392128	0.84[CEU][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1392129	0.85[CEU][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1392130	0.81[CEU][hapmap];0.81[AMR][1000 genomes]
rs1392132	0.81[CEU][hapmap]
rs1587432	0.81[AMR][1000 genomes]
rs1604016	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17417716	0.84[EUR][1000 genomes]
rs4339898	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56169646	0.84[EUR][1000 genomes]
rs61774741	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61776360	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61776375	0.84[EUR][1000 genomes]
rs61776377	0.84[EUR][1000 genomes]
rs6588566	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6669248	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6675850	0.88[CEU][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7513395	0.85[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7544458	0.84[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7546899	0.85[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7555929	0.84[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7556008	0.81[AMR][1000 genomes]
rs904602	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs9787362	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv10184	chr1:55728755-56084833	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv523489	chr1:56038407-56066503	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56037200-56047200	Weak transcription	Esophagus	oesophagus
2	chr1:56039000-56045200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr1:56039000-56045800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:56039000-56046000	Weak transcription	NHLF	lung
5	chr1:56039000-56046800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr1:56039200-56045800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:56039200-56047200	Weak transcription	Psoas Muscle	Psoas
8	chr1:56039400-56045000	Weak transcription	HSMMtube	muscle
9	chr1:56039600-56046200	Weak transcription	NH-A	brain
10	chr1:56040600-56058600	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr1:56041800-56045000	Weak transcription	Osteobl	bone
12	chr1:56041800-56045200	Weak transcription	NHDF-Ad	bronchial
13	chr1:56042000-56045000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:56042000-56046200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr1:56042000-56046400	Weak transcription	Colon Smooth Muscle	Colon
16	chr1:56042000-56046600	Weak transcription	Brain Anterior Caudate	brain
17	chr1:56042000-56047400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr1:56042200-56045000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr1:56042200-56046200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr1:56042200-56046200	Weak transcription	Brain Substantia Nigra	brain
21	chr1:56042200-56046400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:56042200-56046400	Weak transcription	Brain Angular Gyrus	brain
23	chr1:56042200-56046400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr1:56042200-56046600	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr1:56042200-56046600	Weak transcription	Brain Hippocampus Middle	brain
26	chr1:56042200-56049600	Weak transcription	Fetal Muscle Leg	muscle
27	chr1:56042200-56052400	Weak transcription	Right Atrium	heart
28	chr1:56042800-56046400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr1:56042800-56046400	Enhancers	HMEC	breast
30	chr1:56043000-56049600	Weak transcription	Brain Germinal Matrix	brain
31	chr1:56043000-56049800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr1:56043000-56050200	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr1:56043000-56050400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr1:56043400-56046400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr1:56043600-56045000	Enhancers	Fetal Stomach	stomach
36	chr1:56043800-56045000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:56044000-56045400	Enhancers	Fetal Lung	lung
38	chr1:56044400-56051400	Enhancers	Muscle Satellite Cultured Cells	--
39	chr1:56044600-56045400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:56044600-56048400	Enhancers	HSMM	muscle
41	chr1:56044800-56046800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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