Variant report

Variant	rs17502858
Chromosome Location	chr1:225781230-225781231
allele	A/G
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	chr1:225779097..225781482-chr1:225782151..225783761,2	MCF-7	breast:
4	chr1:225726738..225728808-chr1:225780265..225782118,2	K562	blood:

Variant related genes	Relation type
ENSG00000154380	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10429871	0.88[EUR][1000 genomes]
rs11801322	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12027872	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12038893	1.00[CEU][hapmap]
rs12039453	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1340868	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1537877	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1537878	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16845078	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17500089	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17500562	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17500604	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17500639	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17500679	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17500814	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17500944	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17501138	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17501208	1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17501249	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17501775	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17501845	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17501956	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17502068	1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17502075	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17502297	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17502774	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17502823	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17502961	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17503792	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17559267	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17559587	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17560021	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17560215	1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17560579	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17561095	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17561221	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17561228	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17561368	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17561451	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17561781	1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17562010	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]
rs17562052	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17568665	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17569049	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17569145	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17569194	0.90[ASN][1000 genomes]
rs1832229	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1876085	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1876086	1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28617210	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3947140	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6687755	0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73125707	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs954615	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]

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:60 , 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	chr1:225770000-225782000	Weak transcription	Right Atrium	heart
11	chr1:225770000-225783200	Weak transcription	Psoas Muscle	Psoas
12	chr1:225770000-225785200	Weak transcription	Left Ventricle	heart
13	chr1:225770000-225787600	Weak transcription	Fetal Muscle Trunk	muscle
14	chr1:225770800-225781800	Weak transcription	Osteobl	bone
15	chr1:225771000-225784000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:225774800-225793200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr1:225776200-225781400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:225776400-225797200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr1:225777000-225781600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr1:225777000-225793400	Weak transcription	Pancreas	Pancrea
21	chr1:225777800-225783600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:225778400-225784000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr1:225778400-225784400	Weak transcription	Brain Angular Gyrus	brain
24	chr1:225778600-225783600	Weak transcription	Brain Hippocampus Middle	brain
25	chr1:225778600-225785400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr1:225778600-225787600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr1:225778600-225794200	Weak transcription	Brain Substantia Nigra	brain
28	chr1:225779400-225785400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:225779600-225782200	Enhancers	Stomach Smooth Muscle	stomach
30	chr1:225779600-225782600	Enhancers	Colon Smooth Muscle	Colon
31	chr1:225779600-225782600	Enhancers	Rectal Smooth Muscle	rectum
32	chr1:225779600-225783400	Strong transcription	NH-A	brain
33	chr1:225779800-225782200	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr1:225779800-225782400	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr1:225780000-225782200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:225780000-225782400	Genic enhancers	Fetal Lung	lung
37	chr1:225780200-225781600	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr1:225780200-225782200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr1:225780200-225790400	Weak transcription	NHLF	lung
40	chr1:225780200-225794200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:225780400-225786200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr1:225780600-225781600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr1:225780600-225782000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr1:225780800-225781800	Flanking Active TSS	Fetal Heart	heart
45	chr1:225780800-225785000	Weak transcription	Fetal Muscle Leg	muscle
46	chr1:225780800-225815400	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr1:225781000-225781800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:225781000-225782400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr1:225781000-225791400	Weak transcription	Adipose Nuclei	Adipose
50	chr1:225781000-225825400	Weak transcription	Fetal Stomach	stomach

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