Variant report

Variant	rs554671
Chromosome Location	chr6:11545766-11545767
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:11536958..11539680-chr6:11545260..11547548,2	MCF-7	breast:
2	chr6:11537112..11540314-chr6:11541089..11545769,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000205269	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs11751931	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16871371	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17607537	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17607558	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17675742	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17675772	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2140109	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2177158	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2177159	0.85[EUR][1000 genomes]
rs2327440	0.84[JPT][hapmap]
rs34066851	0.86[EUR][1000 genomes]
rs34255222	0.86[EUR][1000 genomes]
rs34336996	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34342746	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34363244	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34486680	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34586980	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34630993	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34678413	0.86[EUR][1000 genomes]
rs34793558	0.85[EUR][1000 genomes]
rs34951511	0.85[EUR][1000 genomes]
rs35074878	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35087778	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35100959	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35250180	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35491413	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35658210	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35877256	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35938392	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36021289	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36023953	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36053861	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36120363	0.86[EUR][1000 genomes]
rs3942485	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4711303	0.94[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4713556	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4713562	0.94[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4713569	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4713577	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs4713579	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs471560	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs471752	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs478147	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs483637	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs490466	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs509971	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs513870	0.80[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];0.85[ASN][1000 genomes]
rs519140	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs524159	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs528679	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs538808	0.98[ASN][1000 genomes]
rs539160	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs552681	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs555034	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs555742	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56055084	0.83[ASN][1000 genomes]
rs566237	0.80[CEU][hapmap];0.83[CHB][hapmap];0.84[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs571683	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs573082	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs574254	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs578507	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs581285	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs586105	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs598907	1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs605058	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs606402	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap]
rs618573	0.80[EUR][1000 genomes]
rs620729	0.80[CEU][hapmap];0.88[CHB][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap]
rs62394918	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62394920	0.86[EUR][1000 genomes]
rs62394921	0.86[EUR][1000 genomes]
rs62394922	0.86[EUR][1000 genomes]
rs62394924	0.80[EUR][1000 genomes]
rs62394925	0.86[EUR][1000 genomes]
rs62394927	0.80[EUR][1000 genomes]
rs62394928	0.80[EUR][1000 genomes]
rs628980	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs637564	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6457608	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs661055	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs663283	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66502560	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67452935	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs675565	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs67807015	0.85[EUR][1000 genomes]
rs678862	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];1.00[ASN][1000 genomes]
rs685384	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs687163	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6904209	0.84[EUR][1000 genomes]
rs6907890	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6907900	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6907944	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6923613	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6923798	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6936326	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs7752671	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs821443	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9348893	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9357151	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9366802	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9368729	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9380321	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9394108	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9394109	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9394115	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9394119	0.84[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	nsv1021078	chr6:10819083-11558560	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv538135	chr6:10819083-11558560	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv432848	chr6:11371614-11560114	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv600989	chr6:11509323-11581990	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
5	nsv1015234	chr6:11545582-11583516	Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs554671	GCNT2	cis	cerebellum	SCAN
rs554671	TMEM170B	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11539600-11547000	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr6:11540200-11547000	Weak transcription	Adipose Nuclei	Adipose
3	chr6:11540200-11547000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr6:11540200-11552000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr6:11540400-11551600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr6:11540400-11552600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:11540600-11566600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr6:11540800-11551200	Weak transcription	Brain Substantia Nigra	brain
9	chr6:11541400-11556000	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr6:11542400-11546400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
11	chr6:11543800-11546000	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr6:11544400-11554400	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr6:11545000-11546400	Weak transcription	Primary B cells from cord blood	blood
14	chr6:11545400-11546000	Enhancers	Brain Anterior Caudate	brain
15	chr6:11545600-11545800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr6:11545600-11545800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
17	chr6:11545600-11554600	Weak transcription	Fetal Brain Female	brain

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