Variant report

Variant	rs28417582
Chromosome Location	chr4:87727556-87727557
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:87726325..87728258-chr4:87729509..87731494,2	MCF-7	breast:

Extended variants
information (count: 186 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:184)

rs_ID	r²[population]
rs10000226	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10000891	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10001010	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10001986	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10002511	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10003989	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10009119	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10009309	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10009603	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10009758	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10009789	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10013048	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10013114	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10013467	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10013878	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10013988	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10015000	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10016082	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10016120	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10016124	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10016456	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10020590	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10021168	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10023163	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10024496	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10024631	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10024860	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10025930	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10026645	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10028003	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10028357	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10028550	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10029055	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10029565	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10030981	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10032126	1.00[EUR][1000 genomes]
rs10032979	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10033029	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10033679	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10084899	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10084902	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10084954	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10212681	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10212723	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10213021	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10213484	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10213632	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1038290	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10470883	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10470933	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10516780	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10516783	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10516784	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11097118	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11097119	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11097120	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11947598	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12171330	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12171331	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12171388	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12171414	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12171415	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12171445	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12171459	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12171474	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12498606	0.95[EUR][1000 genomes]
rs12498681	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12499471	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12499477	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12499575	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12499984	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12499991	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12500797	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12502376	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12504551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12507034	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12507163	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12508339	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12508746	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12509560	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12511153	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12511318	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12512858	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12710827	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13108514	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13108571	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13108581	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13108735	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13109164	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13110760	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13111757	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13112139	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13112150	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13115122	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13115681	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13117481	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13118632	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13120724	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13131069	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13136201	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13136651	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13148078	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13148807	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13149431	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13152382	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1420620	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1420622	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1420623	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17454432	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17454655	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17694358	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17750575	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28409669	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28411302	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28416315	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28421178	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28441099	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28448567	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28455719	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28483600	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28491390	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28502328	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28535818	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28545322	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28548225	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28558568	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28570548	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28572183	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28572787	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28578632	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28587332	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28610135	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28619493	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28623441	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28631999	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28634740	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28645624	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28663463	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28674577	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28682899	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28696860	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28710769	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28785508	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28785868	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28833029	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28846151	0.96[AMR][1000 genomes]
rs28846800	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28868582	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28877076	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34178790	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34320168	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34371873	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35254293	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35323910	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35355289	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35528563	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35915886	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35982123	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs66584788	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67067959	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6817630	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71605612	1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs71605613	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71605614	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71605615	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71605617	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71605618	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71633353	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7664147	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7664860	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7698481	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7699564	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9307022	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9307023	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9307024	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9884784	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9985645	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9990536	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9993492	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9993838	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9994213	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9997271	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9997453	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9999866	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	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv830001	chr4:87585278-87748643	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87635200-87737400	Weak transcription	Fetal Brain Male	brain
2	chr4:87639400-87739200	Weak transcription	A549	lung
3	chr4:87642400-87735800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr4:87661600-87737800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:87661800-87728800	Weak transcription	Pancreas	Pancrea
6	chr4:87689400-87738200	Weak transcription	Gastric	stomach
7	chr4:87690000-87738800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr4:87690800-87736000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr4:87692800-87734200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr4:87694400-87735600	Weak transcription	Stomach Smooth Muscle	stomach
11	chr4:87695600-87728600	Weak transcription	Adipose Nuclei	Adipose
12	chr4:87696800-87733600	Weak transcription	NHLF	lung
13	chr4:87698200-87728600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr4:87698600-87738600	Weak transcription	Brain Angular Gyrus	brain
15	chr4:87712000-87736600	Weak transcription	Fetal Muscle Trunk	muscle
16	chr4:87712400-87728800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr4:87712600-87728600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr4:87712600-87733600	Weak transcription	Lung	lung
19	chr4:87712600-87735800	Weak transcription	Brain Germinal Matrix	brain
20	chr4:87712600-87737600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr4:87712600-87738400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr4:87712600-87751400	Weak transcription	Aorta	Aorta
23	chr4:87712800-87732000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr4:87712800-87736400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr4:87712800-87737000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr4:87712800-87739600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr4:87713200-87728600	Weak transcription	Ovary	ovary
28	chr4:87714400-87731800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr4:87715600-87732600	Weak transcription	Brain Substantia Nigra	brain
30	chr4:87715800-87737400	Weak transcription	Colon Smooth Muscle	Colon
31	chr4:87717200-87737000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr4:87717600-87730800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr4:87717600-87731000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr4:87717800-87732400	Weak transcription	Fetal Thymus	thymus
35	chr4:87718000-87732400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr4:87719200-87738600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr4:87719400-87738000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr4:87719800-87728600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr4:87720000-87728600	Weak transcription	Brain Anterior Caudate	brain
40	chr4:87720000-87728600	Weak transcription	Fetal Intestine Large	intestine
41	chr4:87720000-87736200	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr4:87720800-87732200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr4:87721000-87727600	Weak transcription	Fetal Kidney	kidney
44	chr4:87721800-87733600	Weak transcription	Fetal Stomach	stomach
45	chr4:87722200-87728600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr4:87722200-87728600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr4:87722200-87730600	Weak transcription	Esophagus	oesophagus
48	chr4:87722400-87728600	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr4:87722400-87728800	Weak transcription	Brain Hippocampus Middle	brain
50	chr4:87722600-87736400	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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