Variant report

Variant	rs561929
Chromosome Location	chr15:73599632-73599633
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:73599351..73601141-chr15:73925069..73927572,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000156642	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11072404	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1320241	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1479336	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1620369	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1621216	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1631796	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1678246	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1678247	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16957640	1.00[CEU][hapmap]
rs1871387	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1960423	0.99[ASN][1000 genomes]
rs2619257	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2619258	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2623989	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2623991	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2623992	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2623999	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2624000	0.82[EUR][1000 genomes]
rs2660822	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2660825	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2660828	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2680336	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2680337	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2680342	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2680345	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2680346	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4564531	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4570800	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs471192	1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4776627	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4776629	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs481579	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs484515	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs484544	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];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs489873	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs494493	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs497539	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs499098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs513744	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs525587	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs529004	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs542259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs549377	0.82[CHB][hapmap];0.83[JPT][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs553238	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55787640	0.83[EUR][1000 genomes]
rs6495056	1.00[CEU][hapmap]
rs68053508	0.88[EUR][1000 genomes]
rs68123262	0.83[EUR][1000 genomes]
rs7163504	1.00[CEU][hapmap]
rs7170328	1.00[CEU][hapmap]
rs7177629	0.87[CEU][hapmap];0.83[JPT][hapmap]
rs8037761	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8039308	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9806271	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904343	chr15:73396760-73775043	Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73536200-73602000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr15:73568600-73600800	Strong transcription	Rectal Mucosa Donor 29	rectum
3	chr15:73571200-73601400	Strong transcription	Fetal Stomach	stomach
4	chr15:73586800-73601200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr15:73588800-73601400	Strong transcription	Fetal Intestine Large	intestine
6	chr15:73588800-73601800	Strong transcription	Fetal Intestine Small	intestine
7	chr15:73593200-73601800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr15:73593200-73602000	Strong transcription	Aorta	Aorta
9	chr15:73595400-73600000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr15:73595400-73603800	Weak transcription	Spleen	Spleen
11	chr15:73595600-73601600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr15:73595600-73610200	Weak transcription	Fetal Brain Male	brain
13	chr15:73596200-73599800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr15:73596400-73611000	Weak transcription	Brain Anterior Caudate	brain
15	chr15:73596600-73610000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr15:73596600-73610200	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr15:73596800-73602200	Weak transcription	Lung	lung
18	chr15:73596800-73609600	Weak transcription	Fetal Lung	lung
19	chr15:73596800-73616800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr15:73597000-73600000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr15:73597000-73600000	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr15:73597000-73601000	Weak transcription	Fetal Kidney	kidney
23	chr15:73597000-73601000	Weak transcription	Ovary	ovary
24	chr15:73597000-73606000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr15:73597000-73609600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr15:73597000-73610000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr15:73597200-73602200	Weak transcription	Fetal Muscle Trunk	muscle
28	chr15:73597200-73603600	Weak transcription	Fetal Muscle Leg	muscle
29	chr15:73597400-73603200	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr15:73598000-73610400	Weak transcription	Brain Germinal Matrix	brain
31	chr15:73598200-73601400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr15:73598200-73601600	Strong transcription	Stomach Smooth Muscle	stomach
33	chr15:73598200-73602000	Weak transcription	Gastric	stomach
34	chr15:73598200-73622800	Weak transcription	Right Atrium	heart
35	chr15:73598400-73602000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr15:73598600-73610800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr15:73598800-73600400	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr15:73598800-73601400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr15:73598800-73601400	Weak transcription	Brain Angular Gyrus	brain
40	chr15:73598800-73602000	Weak transcription	Brain Substantia Nigra	brain
41	chr15:73598800-73607400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr15:73598800-73610800	Weak transcription	Brain Hippocampus Middle	brain
43	chr15:73598800-73620000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr15:73599000-73600400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr15:73599200-73600000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr15:73599200-73600000	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr15:73599200-73600600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr15:73599200-73600800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr15:73599200-73600800	Strong transcription	Pancreas	Pancrea
50	chr15:73599400-73601000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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