Variant report

Variant	rs225666
Chromosome Location	chr6:142497476-142497477
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:142492670..142496237-chr6:142496854..142499913,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GJE1-4	chr6:142497360-142497981	NONHSAT115305

Extended variants
information (count: 97 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs11758623	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs178783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225601	0.93[ASN][1000 genomes]
rs225602	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs225604	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs225605	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs225606	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs225618	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs225620	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs225622	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs225623	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs225624	0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs225629	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs225630	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs225631	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs225632	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs225633	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs225634	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs225635	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs225636	0.96[ASN][1000 genomes]
rs225639	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs225640	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs225641	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs225642	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs225643	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs225650	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs225651	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs225652	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs225653	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs225654	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs225655	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs225656	0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs225657	0.83[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs225658	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs225659	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs225660	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs225661	0.92[ASN][1000 genomes]
rs225662	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs225663	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs225664	0.92[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs225665	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs225667	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225668	0.86[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225670	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225672	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225673	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225674	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs225677	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs225678	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs225679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225680	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225682	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225683	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225686	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225687	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225688	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs225689	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs225690	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225692	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225693	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225695	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225696	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225697	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225698	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225701	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs225704	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225705	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225706	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225707	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225708	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225709	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs225710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs225728	0.83[ASN][1000 genomes]
rs4896574	0.91[JPT][hapmap]
rs4896575	0.91[JPT][hapmap]
rs56185739	1.00[ASN][1000 genomes]
rs62430473	0.93[ASN][1000 genomes]
rs62430506	0.85[ASN][1000 genomes]
rs628311	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs638804	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs639658	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7776318	0.81[JPT][hapmap]
rs9321861	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs9389979	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9389980	0.92[CHB][hapmap];0.82[JPT][hapmap]

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:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142470200-142504000	Weak transcription	Spleen	Spleen
2	chr6:142474600-142500800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr6:142474800-142506800	Weak transcription	Hela-S3	cervix
4	chr6:142477200-142500600	Weak transcription	Fetal Brain Male	brain
5	chr6:142477600-142499600	Weak transcription	Stomach Mucosa	stomach
6	chr6:142483200-142499800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr6:142484200-142533800	Weak transcription	Aorta	Aorta
8	chr6:142484400-142498400	Weak transcription	Psoas Muscle	Psoas
9	chr6:142484600-142510000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr6:142486400-142497800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr6:142486600-142498000	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr6:142486800-142497800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr6:142487200-142498000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr6:142487400-142498400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr6:142487400-142499000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr6:142487400-142500200	Strong transcription	Placenta	Placenta
17	chr6:142487600-142498000	Strong transcription	Primary B cells from peripheral blood	blood
18	chr6:142487600-142498000	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr6:142487600-142498400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr6:142487600-142498400	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr6:142487600-142498800	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr6:142487600-142499800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr6:142487600-142500200	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr6:142487800-142499200	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr6:142487800-142499400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr6:142487800-142502200	Strong transcription	HSMM	muscle
27	chr6:142488000-142500000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr6:142489000-142500400	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr6:142489000-142543200	Weak transcription	Small Intestine	intestine
30	chr6:142489200-142507400	Weak transcription	Fetal Heart	heart
31	chr6:142489400-142500800	Weak transcription	K562	blood
32	chr6:142490400-142498000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr6:142490400-142499000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr6:142490600-142499400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr6:142491000-142499600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr6:142491400-142498000	Strong transcription	Dnd41	blood
37	chr6:142491800-142498600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr6:142492000-142499200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr6:142492200-142524800	Weak transcription	Brain Angular Gyrus	brain
40	chr6:142493400-142497600	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr6:142493400-142499600	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr6:142494000-142498000	Weak transcription	Fetal Kidney	kidney
43	chr6:142494600-142499000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr6:142495000-142497800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr6:142495200-142497800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr6:142495200-142498000	Weak transcription	Brain Substantia Nigra	brain
47	chr6:142495200-142498800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr6:142495200-142499000	Weak transcription	Colon Smooth Muscle	Colon
49	chr6:142495400-142497600	Weak transcription	A549	lung
50	chr6:142495400-142497800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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