Variant report

Variant	rs17501956
Chromosome Location	chr1:225735377-225735378
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:225734555..225736207-chr1:225742456..225744694,2	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]
rs11801322	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12027872	1.00[AFR][1000 genomes]
rs12039453	1.00[TSI][hapmap]
rs1340868	1.00[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1537877	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]
rs1537878	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]
rs16845078	1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17500089	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17500562	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17500604	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17500639	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17500679	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17500814	1.00[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17500944	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17501138	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17501208	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17501249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17501775	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]
rs17501845	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17502068	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17502075	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17502297	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17502774	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17502823	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17502858	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17502961	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17503792	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17558869	1.00[CHD][hapmap]
rs17559267	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17559587	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17560021	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17560215	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17560579	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17561095	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17561221	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17561228	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17561368	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17561451	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17561781	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17562010	1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17562052	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17568665	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17569049	1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17569145	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1876085	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1876086	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28617210	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3947140	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6687755	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73125707	0.90[ASN][1000 genomes]
rs954615	1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[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:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225701400-225744400	Weak transcription	HUVEC	blood vessel
2	chr1:225701400-225747000	Weak transcription	Hela-S3	cervix
3	chr1:225705600-225747400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:225707200-225755000	Weak transcription	Gastric	stomach
5	chr1:225717600-225744400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:225717800-225744400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr1:225717800-225745000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr1:225717800-225747400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:225717800-225747400	Weak transcription	Fetal Stomach	stomach
10	chr1:225717800-225758200	Weak transcription	HepG2	liver
11	chr1:225718400-225756400	Weak transcription	NHLF	lung
12	chr1:225722800-225747600	Weak transcription	Fetal Intestine Small	intestine
13	chr1:225723200-225739600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr1:225726800-225744000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr1:225727200-225739200	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr1:225727400-225736200	Weak transcription	HSMMtube	muscle
17	chr1:225727400-225737800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:225727400-225744400	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr1:225727400-225747600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:225727400-225747600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:225727600-225735400	Weak transcription	Brain Anterior Caudate	brain
22	chr1:225727600-225737600	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr1:225727600-225753600	Weak transcription	NHEK	skin
24	chr1:225727800-225735800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:225728000-225753400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:225728400-225735400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:225728800-225737400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr1:225728800-225739200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr1:225730000-225744400	Weak transcription	Fetal Muscle Leg	muscle
30	chr1:225730200-225736600	Weak transcription	Right Atrium	heart
31	chr1:225730200-225737600	Weak transcription	Ovary	ovary
32	chr1:225730200-225747600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:225730200-225753400	Weak transcription	NHDF-Ad	bronchial
34	chr1:225730200-225753600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr1:225730400-225737200	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr1:225730400-225744000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr1:225730600-225737400	Weak transcription	Right Ventricle	heart
38	chr1:225730600-225747600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr1:225730600-225765800	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr1:225730600-225776200	Weak transcription	Pancreas	Pancrea
41	chr1:225732000-225744400	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr1:225732000-225744600	Weak transcription	Fetal Intestine Large	intestine
43	chr1:225732400-225737400	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr1:225732400-225737600	Weak transcription	Psoas Muscle	Psoas
45	chr1:225732400-225763000	Weak transcription	Rectal Smooth Muscle	rectum
46	chr1:225732800-225735400	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr1:225732800-225735400	Weak transcription	Fetal Heart	heart
48	chr1:225733000-225735400	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr1:225733000-225737400	Weak transcription	Colon Smooth Muscle	Colon
50	chr1:225733000-225744400	Weak transcription	Skeletal Muscle Female	skeletal muscle

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