Variant report

Variant	rs6880309
Chromosome Location	chr5:178253945-178253946
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:178248233..178250497-chr5:178253238..178254765,2	K562	blood:
2	chr5:178252394..178254113-chr5:178255346..178258174,3	K562	blood:
3	chr5:178156362..178158364-chr5:178252776..178254974,2	K562	blood:

Variant related genes	Relation type
ENSG00000169131	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10036005	0.93[ASN][1000 genomes]
rs10059914	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10903234	0.88[ASN][1000 genomes]
rs11249579	0.94[ASN][1000 genomes]
rs11249594	0.88[ASN][1000 genomes]
rs11249595	0.88[ASN][1000 genomes]
rs11249596	0.88[ASN][1000 genomes]
rs12515217	0.88[ASN][1000 genomes]
rs12515789	0.88[ASN][1000 genomes]
rs12653675	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12659865	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12659899	1.00[CEU][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13168177	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13171491	0.90[ASN][1000 genomes]
rs13176136	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13185058	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13185213	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13185345	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13186348	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13188572	0.87[ASN][1000 genomes]
rs28516575	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28666448	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35000987	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35120582	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35572924	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35780262	0.88[ASN][1000 genomes]
rs4073382	0.85[ASN][1000 genomes]
rs4073864	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4700796	0.93[ASN][1000 genomes]
rs4701141	0.86[ASN][1000 genomes]
rs4701142	0.91[ASN][1000 genomes]
rs6422327	0.86[ASN][1000 genomes]
rs6600958	0.86[ASN][1000 genomes]
rs6600959	0.93[ASN][1000 genomes]
rs6600962	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6600965	1.00[CEU][hapmap];0.86[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6600966	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6600968	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6600969	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6600970	0.96[ASN][1000 genomes]
rs6600971	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6600972	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6600973	0.96[ASN][1000 genomes]
rs6600974	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6600975	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6600976	1.00[CEU][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6600977	1.00[CEU][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6600978	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6600979	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6861417	0.94[ASN][1000 genomes]
rs6867380	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6869597	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6871640	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6874069	0.83[CEU][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6879858	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6881187	0.81[ASN][1000 genomes]
rs6884341	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6885551	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6887669	0.93[ASN][1000 genomes]
rs6888125	0.92[ASN][1000 genomes]
rs6889638	0.90[ASN][1000 genomes]
rs6892280	0.94[ASN][1000 genomes]
rs6897032	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7447735	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7701596	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7703952	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7709956	0.94[ASN][1000 genomes]
rs7713731	0.92[ASN][1000 genomes]
rs7716645	1.00[CEU][hapmap];0.87[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7716807	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7718276	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7720135	0.88[ASN][1000 genomes]
rs7720550	1.00[CEU][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7722370	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7726476	0.93[ASN][1000 genomes]
rs7735410	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1031206	chr5:178149292-178283614	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv537973	chr5:178149292-178283614	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv883218	chr5:178219855-178349391	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv968861	chr5:178251700-178275142	Weak transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv600453	chr5:178252366-178259787	Enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178236800-178255800	Weak transcription	K562	blood
2	chr5:178252400-178254000	Enhancers	iPS-20b Cell Line	embryonic stem cell
3	chr5:178252400-178254600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr5:178252400-178255000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:178252600-178254200	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr5:178252600-178254400	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr5:178252600-178254400	Enhancers	HMEC	breast
8	chr5:178252600-178254600	Enhancers	NHEK	skin
9	chr5:178252600-178255000	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr5:178252800-178254000	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr5:178252800-178254400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr5:178253200-178255800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr5:178253200-178256000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr5:178253200-178257000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr5:178253200-178257800	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr5:178253400-178254000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr5:178253800-178255000	Enhancers	Breast Myoepithelial Primary Cells	Breast

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