Variant report

Variant	rs239788
Chromosome Location	chr6:54799820-54799821
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:54789461..54791108-chr6:54797681..54800253,2	MCF-7	breast:
2	chr6:54710374..54712137-chr6:54797856..54800336,2	MCF-7	breast:
3	chr6:54793235..54795806-chr6:54798273..54802120,4	MCF-7	breast:
4	chr6:54763489..54765995-chr6:54799336..54801622,2	MCF-7	breast:
5	chr6:54790477..54792574-chr6:54798805..54800751,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168143	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1028423	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1056630	1.00[ASN][1000 genomes]
rs1503137	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs1503150	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16886072	1.00[CHB][hapmap]
rs16886073	1.00[CHB][hapmap]
rs16886088	1.00[CHB][hapmap]
rs16886105	1.00[CHB][hapmap]
rs171226	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1738459	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs183011	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1910352	1.00[CHB][hapmap]
rs2397176	0.92[ASN][1000 genomes]
rs239780	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239787	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239789	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239791	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239793	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239797	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239798	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239799	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239802	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239805	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs239807	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239808	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239810	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239823	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239824	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239827	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239828	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs239829	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239830	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239831	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239832	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239833	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239834	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239835	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239836	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239838	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239839	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239840	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239841	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239842	1.00[CEU][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239843	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239844	0.85[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239845	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239846	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239847	0.87[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239848	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239849	1.00[CEU][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs239851	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs239852	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs239853	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2746440	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35620314	0.84[ASN][1000 genomes]
rs378853	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs398483	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs406149	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41431945	1.00[CHB][hapmap]
rs57835829	1.00[ASN][1000 genomes]
rs59689523	0.92[ASN][1000 genomes]
rs6917766	1.00[ASN][1000 genomes]
rs73431470	0.92[ASN][1000 genomes]
rs7453441	1.00[CHB][hapmap]
rs7739951	1.00[CHB][hapmap]
rs7743188	1.00[CHB][hapmap]
rs7749972	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7774568	0.84[ASN][1000 genomes]
rs9349735	1.00[CHB][hapmap]
rs9367588	1.00[CHB][hapmap]
rs9367589	1.00[CHB][hapmap]
rs9367596	1.00[CHB][hapmap]
rs9370335	1.00[CHB][hapmap]
rs9382377	1.00[CHB][hapmap]
rs9382388	1.00[CHB][hapmap]
rs9395992	1.00[CHB][hapmap]
rs9475077	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885900	chr6:54517968-54852462	Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2763553	chr6:54687979-54820487	Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54785600-54805000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr6:54786800-54800000	Weak transcription	Hela-S3	cervix
3	chr6:54789800-54810200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr6:54790000-54800200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr6:54797000-54811800	Weak transcription	Esophagus	oesophagus
6	chr6:54797400-54800000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:54797600-54804600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr6:54798000-54804600	Weak transcription	Duodenum Mucosa	Duodenum
9	chr6:54798800-54804800	Weak transcription	Fetal Intestine Large	intestine
10	chr6:54798800-54815600	Weak transcription	Fetal Intestine Small	intestine
11	chr6:54799000-54800200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr6:54799200-54800000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:54799400-54801400	Enhancers	HMEC	breast
14	chr6:54799600-54801600	Enhancers	NHEK	skin
15	chr6:54799800-54800400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:54799800-54800800	Enhancers	Monocytes-CD14+_RO01746	blood

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