Variant report

Variant	rs17562010
Chromosome Location	chr1:225782233-225782234
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225780964..225783370-chr1:225840747..225843088,2	MCF-7	breast:
2	chr1:225777393..225780281-chr1:225780667..225783094,2	K562	blood:
3	chr1:225781721..225783734-chr1:225964574..225966538,3	MCF-7	breast:
4	chr1:225779097..225781482-chr1:225782151..225783761,2	MCF-7	breast:
5	chr1:225774139..225778253-chr1:225781548..225783833,3	K562	blood:

Variant related genes	Relation type
ENSG00000154380	Chromatin interaction
ENSG00000143742	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10429871	0.88[EUR][1000 genomes]
rs11801322	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12027872	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12039453	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1340868	1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1537877	1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1537878	1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16845078	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17500089	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs17500562	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17500604	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17500639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17500679	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17500814	1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17500944	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17501138	1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17501208	1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17501249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17501775	1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17501845	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17501956	1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17502068	1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17502075	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17502297	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17502774	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17502823	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17502858	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17502961	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17503792	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17559267	1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17559587	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17560021	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17560215	1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17560579	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17561095	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17561221	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17561228	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17561368	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17561451	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17561781	1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17562052	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17568665	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17569049	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17569145	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17569194	1.00[ASN][1000 genomes]
rs1832229	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1876085	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1876086	1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28617210	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3947140	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6687755	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73125707	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs954615	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv832714	chr1:225592333-225805396	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv832725	chr1:225726998-225910121	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225748800-225799400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:225749200-225783800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:225759600-225787600	Weak transcription	Fetal Intestine Small	intestine
4	chr1:225760000-225820600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:225766400-225783600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:225768600-225787800	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr1:225768800-225805600	Weak transcription	Aorta	Aorta
8	chr1:225769000-225783000	Weak transcription	HSMMtube	muscle
9	chr1:225769200-225783200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr1:225770000-225783200	Weak transcription	Psoas Muscle	Psoas
11	chr1:225770000-225785200	Weak transcription	Left Ventricle	heart
12	chr1:225770000-225787600	Weak transcription	Fetal Muscle Trunk	muscle
13	chr1:225771000-225784000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:225774800-225793200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr1:225776400-225797200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr1:225777000-225793400	Weak transcription	Pancreas	Pancrea
17	chr1:225777800-225783600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:225778400-225784000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr1:225778400-225784400	Weak transcription	Brain Angular Gyrus	brain
20	chr1:225778600-225783600	Weak transcription	Brain Hippocampus Middle	brain
21	chr1:225778600-225785400	Weak transcription	Brain Cingulate Gyrus	brain
22	chr1:225778600-225787600	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr1:225778600-225794200	Weak transcription	Brain Substantia Nigra	brain
24	chr1:225779400-225785400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:225779600-225782600	Enhancers	Colon Smooth Muscle	Colon
26	chr1:225779600-225782600	Enhancers	Rectal Smooth Muscle	rectum
27	chr1:225779600-225783400	Strong transcription	NH-A	brain
28	chr1:225779800-225782400	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr1:225780000-225782400	Genic enhancers	Fetal Lung	lung
30	chr1:225780200-225790400	Weak transcription	NHLF	lung
31	chr1:225780200-225794200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr1:225780400-225786200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr1:225780800-225785000	Weak transcription	Fetal Muscle Leg	muscle
34	chr1:225780800-225815400	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr1:225781000-225782400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr1:225781000-225791400	Weak transcription	Adipose Nuclei	Adipose
37	chr1:225781000-225825400	Weak transcription	Fetal Stomach	stomach
38	chr1:225781200-225782400	Enhancers	Right Ventricle	heart
39	chr1:225781200-225783000	Weak transcription	Fetal Brain Male	brain
40	chr1:225781200-225784000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr1:225781200-225785600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr1:225781200-225793200	Weak transcription	Ovary	ovary
43	chr1:225781400-225783400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr1:225781600-225782400	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr1:225781800-225784000	Weak transcription	A549	lung
46	chr1:225781800-225784800	Enhancers	Fetal Heart	heart
47	chr1:225782000-225783800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr1:225782000-225791200	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr1:225782000-225795000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr1:225782200-225782400	Enhancers	HUES48 Cell Line	embryonic stem cell

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