Variant report

Variant	rs225661
Chromosome Location	chr6:142490107-142490108
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs11758623	0.92[ASN][1000 genomes]
rs178783	0.90[ASN][1000 genomes]
rs225601	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs225602	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs225606	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs225618	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs225622	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs225623	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs225624	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs225628	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs225629	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs225630	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs225631	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs225632	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs225633	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs225634	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs225635	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs225636	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs225637	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs225639	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs225640	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs225641	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs225642	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs225643	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs225650	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225651	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225652	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225653	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs225654	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225655	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225656	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs225657	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs225658	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225659	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs225660	0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225662	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225663	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225664	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225665	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225666	0.92[ASN][1000 genomes]
rs225667	0.92[ASN][1000 genomes]
rs225668	0.92[ASN][1000 genomes]
rs225670	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs225671	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs225672	0.92[ASN][1000 genomes]
rs225673	0.92[ASN][1000 genomes]
rs225674	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs225675	0.90[ASN][1000 genomes]
rs225676	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs225677	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs225678	0.87[ASN][1000 genomes]
rs225679	0.90[ASN][1000 genomes]
rs225680	0.90[ASN][1000 genomes]
rs225682	0.90[ASN][1000 genomes]
rs225683	0.90[ASN][1000 genomes]
rs225684	0.90[ASN][1000 genomes]
rs225685	0.90[ASN][1000 genomes]
rs225686	0.90[ASN][1000 genomes]
rs225687	0.90[ASN][1000 genomes]
rs225689	0.89[ASN][1000 genomes]
rs225690	0.90[ASN][1000 genomes]
rs225692	0.90[ASN][1000 genomes]
rs225693	0.90[ASN][1000 genomes]
rs225695	0.90[ASN][1000 genomes]
rs225696	0.90[ASN][1000 genomes]
rs225697	0.90[ASN][1000 genomes]
rs225698	0.90[ASN][1000 genomes]
rs225700	0.90[ASN][1000 genomes]
rs225701	0.90[ASN][1000 genomes]
rs225702	0.87[ASN][1000 genomes]
rs225704	0.90[ASN][1000 genomes]
rs225705	0.90[ASN][1000 genomes]
rs225706	0.90[ASN][1000 genomes]
rs225707	0.90[ASN][1000 genomes]
rs225708	0.90[ASN][1000 genomes]
rs225709	0.88[ASN][1000 genomes]
rs225710	0.88[ASN][1000 genomes]
rs225728	0.80[ASN][1000 genomes]
rs56185739	0.92[ASN][1000 genomes]
rs62430473	0.88[ASN][1000 genomes]
rs62430506	0.81[ASN][1000 genomes]
rs628311	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs638804	0.87[ASN][1000 genomes]
rs639658	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886732	chr6:142290338-142536049	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv886733	chr6:142316672-142514226	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv886734	chr6:142347611-142523865	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv830824	chr6:142361107-142544929	Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv886736	chr6:142365171-142523865	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142470200-142491800	Weak transcription	Fetal Stomach	stomach
2	chr6:142470200-142493600	Weak transcription	HSMMtube	muscle
3	chr6:142470200-142504000	Weak transcription	Spleen	Spleen
4	chr6:142474600-142500800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr6:142474800-142506800	Weak transcription	Hela-S3	cervix
6	chr6:142477200-142500600	Weak transcription	Fetal Brain Male	brain
7	chr6:142477600-142499600	Weak transcription	Stomach Mucosa	stomach
8	chr6:142477800-142491800	Weak transcription	NHLF	lung
9	chr6:142479400-142491800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:142481400-142494400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr6:142481600-142497000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr6:142481800-142495000	Weak transcription	Gastric	stomach
13	chr6:142483200-142499800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr6:142484200-142533800	Weak transcription	Aorta	Aorta
15	chr6:142484400-142491800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr6:142484400-142494400	Weak transcription	Fetal Lung	lung
17	chr6:142484400-142498400	Weak transcription	Psoas Muscle	Psoas
18	chr6:142484600-142491000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr6:142484600-142493400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr6:142484600-142494400	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr6:142484600-142510000	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr6:142486400-142495000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr6:142486400-142497800	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr6:142486600-142493600	Weak transcription	Fetal Kidney	kidney
25	chr6:142486600-142494400	Weak transcription	HMEC	breast
26	chr6:142486600-142498000	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr6:142486800-142492800	Weak transcription	Brain Substantia Nigra	brain
28	chr6:142486800-142496200	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr6:142486800-142497800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr6:142487000-142496200	Strong transcription	Fetal Thymus	thymus
31	chr6:142487200-142498000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:142487400-142495600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
33	chr6:142487400-142495800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr6:142487400-142496200	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr6:142487400-142497000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr6:142487400-142498400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr6:142487400-142499000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr6:142487400-142500200	Strong transcription	Placenta	Placenta
39	chr6:142487600-142490400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr6:142487600-142492000	Strong transcription	Liver	Liver
41	chr6:142487600-142492200	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr6:142487600-142496200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr6:142487600-142496400	Strong transcription	Osteobl	bone
44	chr6:142487600-142497200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr6:142487600-142498000	Strong transcription	Primary B cells from peripheral blood	blood
46	chr6:142487600-142498000	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr6:142487600-142498400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr6:142487600-142498400	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr6:142487600-142498800	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr6:142487600-142499800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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