Variant report

Variant	rs954615
Chromosome Location	chr1:225795764-225795765
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225792350..225796305-chr1:225796696..225799620,4	MCF-7	breast:
2	chr1:225794722..225796707-chr1:225839799..225842558,2	MCF-7	breast:
3	chr1:225790028..225792726-chr1:225793823..225796331,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000154380	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]
rs17562010	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]
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]

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:73 , 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	chr1:225760000-225820600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:225768800-225805600	Weak transcription	Aorta	Aorta
4	chr1:225776400-225797200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr1:225780800-225815400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:225781000-225825400	Weak transcription	Fetal Stomach	stomach
7	chr1:225782400-225806200	Weak transcription	Right Ventricle	heart
8	chr1:225784200-225807800	Weak transcription	Fetal Brain Male	brain
9	chr1:225785200-225800000	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr1:225788400-225796200	Weak transcription	Fetal Muscle Trunk	muscle
11	chr1:225791200-225798800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:225791400-225796600	Weak transcription	Brain Angular Gyrus	brain
13	chr1:225791600-225796600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr1:225791600-225799600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:225791600-225802000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr1:225792000-225799600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr1:225792000-225805000	Weak transcription	NHDF-Ad	bronchial
18	chr1:225792200-225800000	Weak transcription	Hela-S3	cervix
19	chr1:225792800-225799600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:225793000-225796600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr1:225793000-225799200	Weak transcription	NHEK	skin
22	chr1:225793200-225795800	Enhancers	Right Atrium	heart
23	chr1:225793200-225799600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr1:225793600-225798400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr1:225793600-225799400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:225793600-225813200	Weak transcription	Left Ventricle	heart
27	chr1:225793600-225813800	Weak transcription	NH-A	brain
28	chr1:225794200-225795800	Enhancers	Brain Substantia Nigra	brain
29	chr1:225794400-225795800	Enhancers	Fetal Lung	lung
30	chr1:225794400-225800000	Weak transcription	Spleen	Spleen
31	chr1:225794600-225796400	Enhancers	Osteobl	bone
32	chr1:225794600-225796800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:225794600-225797000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:225794600-225800000	Weak transcription	Pancreas	Pancrea
35	chr1:225794600-225813200	Weak transcription	Lung	lung
36	chr1:225794800-225795800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:225794800-225795800	Enhancers	Brain Germinal Matrix	brain
38	chr1:225794800-225797200	Enhancers	Colon Smooth Muscle	Colon
39	chr1:225794800-225797400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr1:225794800-225798600	Enhancers	Muscle Satellite Cultured Cells	--
41	chr1:225795000-225795800	Enhancers	Brain Anterior Caudate	brain
42	chr1:225795000-225795800	Enhancers	Brain Hippocampus Middle	brain
43	chr1:225795000-225796000	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr1:225795000-225796000	Enhancers	Fetal Heart	heart
45	chr1:225795000-225797200	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr1:225795000-225797200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:225795000-225797200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr1:225795000-225797400	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr1:225795000-225797400	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr1:225795000-225806000	Weak transcription	Small Intestine	intestine

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