Variant report

Variant	rs1574154
Chromosome Location	chr3:119627247-119627248
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119626680..119629213-chr3:119811810..119814133,3	MCF-7	breast:
2	chr3:119626271..119628027-chr3:119811718..119813325,2	MCF-7	breast:
3	chr3:119607000..119608720-chr3:119626179..119628022,2	MCF-7	breast:
4	chr3:119626669..119629157-chr3:119817976..119820663,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000242622	Chromatin interaction
ENSG00000082701	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10433404	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10934500	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10934502	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10934503	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10934505	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10934506	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10934507	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs1154595	0.87[JPT][hapmap]
rs11915717	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11917714	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12053912	0.82[CEU][hapmap]
rs12054090	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12108149	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12629015	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12630592	0.87[JPT][hapmap]
rs12630829	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12634476	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12634889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12635018	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12638973	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13314595	0.89[YRI][hapmap]
rs13321783	0.87[JPT][hapmap]
rs16830567	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16830689	0.84[YRI][hapmap]
rs1719889	0.90[YRI][hapmap]
rs1719894	0.87[JPT][hapmap]
rs17204878	0.87[JPT][hapmap]
rs1732170	0.91[JPT][hapmap]
rs1870931	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1980718	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2199503	0.82[JPT][hapmap]
rs2276707	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2319398	0.87[JPT][hapmap]
rs2319399	0.87[JPT][hapmap]
rs28536662	0.87[JPT][hapmap]
rs2873950	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28831519	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3107669	0.87[JPT][hapmap]
rs334533	0.87[JPT][hapmap]
rs334535	0.92[YRI][hapmap]
rs334559	0.82[YRI][hapmap]
rs334563	0.87[JPT][hapmap]
rs3732359	0.87[JPT][hapmap]
rs3732360	0.87[JPT][hapmap]
rs3732361	0.91[JPT][hapmap]
rs3814057	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3814058	1.00[CEU][hapmap];0.96[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4072520	0.82[YRI][hapmap]
rs4261913	0.83[JPT][hapmap]
rs4340737	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4624596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4687890	0.87[JPT][hapmap]
rs4687893	0.87[JPT][hapmap]
rs4688042	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]
rs4688046	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4688047	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4688053	0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4688054	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4688059	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.88[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs56728675	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57939147	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58493895	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58863896	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs60235167	0.88[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs60389731	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60393216	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62264706	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62264708	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62264714	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62264734	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62264739	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62264742	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62264743	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62264747	0.89[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs62264749	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs62266274	0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs62266277	0.87[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs62266281	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6438552	0.87[JPT][hapmap]
rs6438553	0.87[JPT][hapmap]
rs6769435	0.82[YRI][hapmap]
rs6770314	0.92[YRI][hapmap]
rs6773751	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6781942	0.87[JPT][hapmap]
rs6782799	0.91[JPT][hapmap]
rs6784598	0.91[JPT][hapmap]
rs6790751	0.89[YRI][hapmap]
rs6792572	0.87[JPT][hapmap]
rs6795653	0.87[JPT][hapmap]
rs6797459	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6800622	0.87[JPT][hapmap]
rs6805251	0.86[JPT][hapmap]
rs6808874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7431209	0.86[JPT][hapmap]
rs7617372	0.89[YRI][hapmap]
rs7620750	0.89[YRI][hapmap]
rs7633279	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]
rs7639388	1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[JPT][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7644234	0.87[JPT][hapmap]
rs7652172	0.85[YRI][hapmap]
rs9813864	0.91[JPT][hapmap]
rs9851174	0.92[YRI][hapmap]
rs9873477	0.87[JPT][hapmap]
rs9878473	0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv829696	chr3:119567659-119711405	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119546000-119663400	Weak transcription	Lung	lung
2	chr3:119569400-119629400	Weak transcription	Esophagus	oesophagus
3	chr3:119574600-119631600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:119582400-119629400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr3:119582600-119627400	Weak transcription	Right Ventricle	heart
6	chr3:119583800-119630400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr3:119597600-119659000	Weak transcription	Gastric	stomach
8	chr3:119604800-119627800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr3:119608000-119627800	Weak transcription	Left Ventricle	heart
10	chr3:119608000-119643600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:119608200-119627400	Weak transcription	Thymus	Thymus
12	chr3:119608200-119639200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:119608200-119677800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr3:119608400-119629800	Weak transcription	Fetal Brain Female	brain
15	chr3:119608600-119629200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:119608600-119630000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr3:119608600-119630000	Weak transcription	Fetal Muscle Leg	muscle
18	chr3:119608800-119629800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr3:119609000-119629600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:119609200-119630000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr3:119611200-119630200	Weak transcription	Psoas Muscle	Psoas
22	chr3:119611200-119643400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr3:119611200-119667000	Weak transcription	Pancreas	Pancrea
24	chr3:119611400-119627400	Weak transcription	Brain Angular Gyrus	brain
25	chr3:119611400-119627400	Weak transcription	Brain Substantia Nigra	brain
26	chr3:119611400-119627600	Weak transcription	Brain Anterior Caudate	brain
27	chr3:119611400-119627800	Weak transcription	Aorta	Aorta
28	chr3:119611400-119627800	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr3:119611400-119629400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr3:119611400-119629400	Weak transcription	Stomach Smooth Muscle	stomach
31	chr3:119611400-119630000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr3:119611400-119630200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr3:119611400-119630600	Weak transcription	Small Intestine	intestine
34	chr3:119611400-119631000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr3:119611400-119632200	Weak transcription	Brain Cingulate Gyrus	brain
36	chr3:119611400-119632200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr3:119611400-119634600	Weak transcription	Spleen	Spleen
38	chr3:119611400-119642000	Weak transcription	Fetal Brain Male	brain
39	chr3:119611400-119649400	Weak transcription	Brain Hippocampus Middle	brain
40	chr3:119611400-119682200	Weak transcription	HSMMtube	muscle
41	chr3:119611600-119627400	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr3:119611600-119629600	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr3:119613000-119637400	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr3:119614200-119645200	Weak transcription	K562	blood
45	chr3:119617400-119628600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr3:119617400-119631000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:119618200-119629600	Weak transcription	NHEK	skin
48	chr3:119618400-119627400	Weak transcription	Fetal Lung	lung
49	chr3:119618400-119627800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr3:119618400-119631600	Weak transcription	HUES6 Cell Line	embryonic stem cell

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