Variant report

Variant	rs55654955
Chromosome Location	chr7:69135716-69135717
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 155 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:147)

rs_ID	r²[population]
rs1000874	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10085600	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10216097	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10229336	0.85[EUR][1000 genomes]
rs10229578	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10229588	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10230356	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10230750	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10233869	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10234831	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10236103	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10238307	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10239569	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10240462	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10242206	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10243408	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10244001	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10244128	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10244247	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10244885	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10245493	0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10245690	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10247386	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10248237	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10254086	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10255563	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10255613	0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10256311	0.81[ASN][1000 genomes]
rs10256512	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10256943	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10257587	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10261380	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10263467	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10268221	0.92[AMR][1000 genomes]
rs10268457	0.92[AMR][1000 genomes]
rs10268729	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10269267	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10272781	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10274099	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10274419	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10275112	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10275721	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10276664	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10278978	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10279669	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10279708	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10280018	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10281575	0.92[AMR][1000 genomes]
rs10281579	0.92[AMR][1000 genomes]
rs10452705	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10487943	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10950193	0.88[EUR][1000 genomes]
rs11762049	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11762487	0.85[EUR][1000 genomes]
rs11764277	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11764717	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11769033	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11769738	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11770241	0.88[EUR][1000 genomes]
rs11771751	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11771899	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11772602	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11773581	0.92[AMR][1000 genomes]
rs11975481	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11975506	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11979745	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17140693	0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs17140755	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17140759	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17140783	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17140817	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17140884	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17140938	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17353920	0.84[EUR][1000 genomes]
rs17457910	0.84[EUR][1000 genomes]
rs17458713	0.84[EUR][1000 genomes]
rs2052124	0.84[EUR][1000 genomes]
rs2068718	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28393394	0.85[EUR][1000 genomes]
rs28493290	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28524600	0.81[ASN][1000 genomes]
rs28577243	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2865804	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28812289	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34080361	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3735260	0.85[ASN][1000 genomes]
rs3800979	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs41379648	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4305786	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55693719	0.81[ASN][1000 genomes]
rs55756263	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55847506	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs55880824	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56800568	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57493471	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58626042	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58666988	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58863846	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61370051	0.82[EUR][1000 genomes]
rs61424317	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61692535	0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs61744589	0.83[ASN][1000 genomes]
rs62454937	0.81[ASN][1000 genomes]
rs62454938	0.81[ASN][1000 genomes]
rs6460525	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6945524	0.84[EUR][1000 genomes]
rs6947326	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6950638	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6951770	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6958450	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6962237	0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6962338	0.84[EUR][1000 genomes]
rs6967788	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6968426	0.85[EUR][1000 genomes]
rs6975211	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6977472	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6980305	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs717266	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs719294	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73154605	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73155227	0.81[ASN][1000 genomes]
rs73164795	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73166559	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73167506	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73168739	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73168740	0.93[EUR][1000 genomes]
rs73168747	0.85[EUR][1000 genomes]
rs73168758	0.85[EUR][1000 genomes]
rs73170834	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73170852	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73170857	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73170864	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73172903	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7357113	0.81[ASN][1000 genomes]
rs740946	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7777243	0.81[EUR][1000 genomes]
rs7777269	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7777621	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7780835	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7781664	0.85[EUR][1000 genomes]
rs7784950	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7787342	0.81[ASN][1000 genomes]
rs7801209	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7810982	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs917718	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs917725	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9690769	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023885	chr7:68894896-69158290	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv538915	chr7:68894896-69158290	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv916011	chr7:68942155-69330800	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv428169	chr7:69021482-69196743	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv831021	chr7:69122169-69364491	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv1021538	chr7:69130236-69575753	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv538917	chr7:69130236-69575753	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv817276	chr7:69130237-69736834	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:69125000-69142000	Weak transcription	Fetal Stomach	stomach
2	chr7:69125000-69142400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr7:69129000-69139800	Weak transcription	Fetal Lung	lung
4	chr7:69134000-69137400	Weak transcription	Fetal Brain Male	brain
5	chr7:69134600-69136600	Enhancers	GM12878-XiMat	blood
6	chr7:69134800-69135800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr7:69134800-69135800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
8	chr7:69134800-69136000	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr7:69134800-69136200	Enhancers	Fetal Brain Female	brain
10	chr7:69134800-69136400	Enhancers	Colon Smooth Muscle	Colon
11	chr7:69134800-69136400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr7:69134800-69136800	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr7:69135000-69135800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr7:69135000-69135800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr7:69135000-69135800	Enhancers	Brain Substantia Nigra	brain
16	chr7:69135000-69135800	Enhancers	Fetal Thymus	thymus
17	chr7:69135000-69136000	Enhancers	Brain Anterior Caudate	brain
18	chr7:69135000-69136000	Enhancers	Ovary	ovary
19	chr7:69135000-69136200	Enhancers	Placenta	Placenta
20	chr7:69135000-69136200	Enhancers	Placenta Amnion	Placenta Amnion
21	chr7:69135000-69136200	Enhancers	Rectal Smooth Muscle	rectum
22	chr7:69135000-69136600	Enhancers	Stomach Smooth Muscle	stomach
23	chr7:69135000-69136800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr7:69135000-69136800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr7:69135200-69135800	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr7:69135200-69135800	Enhancers	Brain Hippocampus Middle	brain
27	chr7:69135200-69136000	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr7:69135200-69136000	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr7:69135200-69136400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr7:69135200-69136400	Enhancers	Adipose Nuclei	Adipose
31	chr7:69135200-69138600	Weak transcription	Brain Angular Gyrus	brain
32	chr7:69135400-69139000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr7:69135400-69141600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr7:69135400-69142800	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr7:69135600-69136000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr7:69135600-69136000	Weak transcription	Brain Germinal Matrix	brain
37	chr7:69135600-69136000	Enhancers	Psoas Muscle	Psoas
38	chr7:69135600-69136200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr7:69135600-69136200	Enhancers	Brain Cingulate Gyrus	brain
40	chr7:69135600-69137600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr7:69135600-69139200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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