Variant report

Variant	rs200982
Chromosome Location	chr6:27831244-27831245
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:27098113..27100606-chr6:27830587..27832158,2	K562	blood:
2	chr6:26171577..26173697-chr6:27830155..27831800,2	MCF-7	breast:
3	chr6:27829699..27832078-chr8:101028376..101031173,2	MCF-7	breast:
4	chr6:27113113..27117592-chr6:27831181..27837403,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197903	Chromatin interaction
ENSG00000184825	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000265565	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs175597	0.82[YRI][hapmap]
rs187995	1.00[EUR][1000 genomes]
rs200470	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs200472	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs200487	0.93[YRI][hapmap]
rs200947	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs200948	0.88[YRI][hapmap]
rs200955	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs200959	0.86[YRI][hapmap];1.00[EUR][1000 genomes]
rs200965	0.83[YRI][hapmap]
rs200984	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs200989	0.82[YRI][hapmap]
rs201003	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs201005	1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56342784	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59716769	1.00[EUR][1000 genomes]
rs7740062	1.00[EUR][1000 genomes]
rs9468198	1.00[EUR][1000 genomes]
rs9468205	1.00[EUR][1000 genomes]
rs9468228	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022797	chr6:27396961-27864277	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	390 gene(s)	inside rSNPs	diseases
2	nsv432858	chr6:27719375-28011652	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	387 gene(s)	inside rSNPs	diseases
3	nsv1017440	chr6:27734824-27864277	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	370 gene(s)	inside rSNPs	diseases
4	nsv1022173	chr6:27734824-27959408	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
5	nsv883512	chr6:27748631-27969004	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
6	nsv601208	chr6:27810626-27969004	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	237 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs200982	Hs.158943	cis	multi-tissue	Pritchard

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27808000-27831800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr6:27822800-27831800	Weak transcription	Primary B cells from peripheral blood	blood
3	chr6:27824000-27831800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:27829000-27831800	Weak transcription	Right Atrium	heart
5	chr6:27830000-27831800	Weak transcription	Dnd41	blood
6	chr6:27830200-27831400	Enhancers	Hela-S3	cervix
7	chr6:27830200-27831600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr6:27830200-27831600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr6:27830200-27831800	Weak transcription	Primary B cells from cord blood	blood
10	chr6:27830400-27832200	Flanking Active TSS	GM12878-XiMat	blood
11	chr6:27830600-27831800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:27830600-27831800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr6:27830800-27831800	Weak transcription	NH-A	brain
14	chr6:27830800-27831800	Weak transcription	NHEK	skin
15	chr6:27830800-27832200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:27830800-27835800	Active TSS	K562	blood
17	chr6:27831000-27831400	Enhancers	NHDF-Ad	bronchial
18	chr6:27831000-27831800	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr6:27831000-27831800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr6:27831200-27831400	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr6:27831200-27831800	Active TSS	Fetal Thymus	thymus
22	chr6:27831200-27832800	Weak transcription	HepG2	liver
23	chr6:27831200-27835800	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr6:27831200-27835800	Active TSS	H9 Cell Line	embryonic stem cell

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