Variant report

Variant	rs2793259
Chromosome Location	chr6:5044769-5044770
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:5041855..5045145-chr6:5046527..5050551,4	K562	blood:
2	chr6:5041855..5045145-chr6:5046527..5048864,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RPP40-1	chr6:5044719-5047759	XLOC_005592

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11967778	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11967814	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12200195	0.82[ASN][1000 genomes]
rs1627212	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs17139235	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1771873	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1771874	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1815673	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1815674	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1815675	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2002380	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2764150	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap]
rs2764153	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2764154	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2764189	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2793239	1.00[JPT][hapmap]
rs2793252	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2793253	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2793254	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2793256	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2793257	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2793258	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2994695	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2994696	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4246072	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4281005	0.85[AMR][1000 genomes]
rs57919800	0.89[ASN][1000 genomes]
rs59552394	0.89[ASN][1000 genomes]
rs62385159	0.82[ASN][1000 genomes]
rs62386470	0.82[ASN][1000 genomes]
rs62386471	0.89[ASN][1000 genomes]
rs726743	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs754334	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs808734	0.83[GIH][hapmap]
rs811259	0.82[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs877229	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs9378925	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2422499	chr6:4745428-5073222	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv830577	chr6:4834567-5050544	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv462622	chr6:4904380-5172009	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv600871	chr6:4904380-5172009	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv1033905	chr6:4955826-5080904	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv600872	chr6:4975313-5342190	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	nsv1031837	chr6:4996667-5418726	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
9	nsv1017380	chr6:5007870-5152551	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2793259	FOXF2	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5027200-5047200	Weak transcription	Adipose Nuclei	Adipose
2	chr6:5033400-5046000	Weak transcription	Fetal Intestine Small	intestine
3	chr6:5033400-5048600	Weak transcription	Aorta	Aorta
4	chr6:5034400-5045200	Weak transcription	Fetal Stomach	stomach
5	chr6:5034800-5045600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr6:5034800-5047400	Weak transcription	Esophagus	oesophagus
7	chr6:5035000-5047400	Weak transcription	Primary B cells from cord blood	blood
8	chr6:5035400-5047800	Weak transcription	Primary B cells from peripheral blood	blood
9	chr6:5036600-5044800	Weak transcription	Primary hematopoietic stem cells	blood
10	chr6:5037000-5050800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:5037200-5044800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr6:5037200-5045200	Weak transcription	Fetal Muscle Leg	muscle
13	chr6:5037200-5046000	Weak transcription	Fetal Muscle Trunk	muscle
14	chr6:5040600-5044800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr6:5041000-5045200	Weak transcription	Primary T cells from cord blood	blood
16	chr6:5043000-5045600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr6:5043800-5048400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr6:5044000-5046600	Weak transcription	Ovary	ovary

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