Variant report

Variant	rs582008
Chromosome Location	chr6:4104567-4104568
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:4101592..4105283-chr6:4133279..4135546,3	K562	blood:

Variant related genes	Relation type
ENSG00000198721	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs101418	0.80[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs11755877	0.80[CHB][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs1204951	0.84[ASN][1000 genomes]
rs2326408	0.91[ASN][1000 genomes]
rs2745455	0.82[ASN][1000 genomes]
rs2783063	0.80[CHB][hapmap];0.82[CHD][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs2783073	0.91[ASN][1000 genomes]
rs28878015	1.00[ASN][1000 genomes]
rs4959271	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs583782	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs583881	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs584585	0.84[CHB][hapmap];0.80[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs592953	0.80[CHB][hapmap]
rs593291	0.80[CHB][hapmap]
rs594662	0.80[CHB][hapmap]
rs595413	0.80[CHB][hapmap]
rs608195	0.80[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs611500	0.91[ASN][1000 genomes]
rs612022	0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs612477	0.86[ASN][1000 genomes]
rs613028	0.88[ASN][1000 genomes]
rs613260	0.91[ASN][1000 genomes]
rs613709	0.91[ASN][1000 genomes]
rs617604	0.82[ASN][1000 genomes]
rs617790	0.85[CHB][hapmap];0.80[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs619439	0.85[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs619483	0.80[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs619873	0.91[ASN][1000 genomes]
rs620484	0.85[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs621205	0.99[ASN][1000 genomes]
rs626080	0.85[CHD][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs627259	0.86[ASN][1000 genomes]
rs629362	0.85[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs633290	0.85[CHB][hapmap];0.80[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs634114	0.80[CHB][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs634698	0.89[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs634970	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs638329	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.88[MEX][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs639905	0.80[CHB][hapmap]
rs643232	0.80[CHB][hapmap];0.80[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs646385	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs648900	0.91[ASN][1000 genomes]
rs649725	0.85[CHB][hapmap];0.80[CHD][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs659025	0.84[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs659051	1.00[ASN][1000 genomes]
rs659305	0.85[CHB][hapmap];0.80[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs660560	0.85[CHB][hapmap];0.80[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs660957	1.00[ASN][1000 genomes]
rs661404	0.85[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs661657	0.84[ASN][1000 genomes]
rs662834	0.80[CHB][hapmap];0.83[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs664299	0.89[ASN][1000 genomes]
rs664635	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs664898	1.00[ASN][1000 genomes]
rs665894	0.82[ASN][1000 genomes]
rs666254	0.80[CHB][hapmap]
rs668070	0.81[ASN][1000 genomes]
rs671364	0.80[CHB][hapmap]
rs674543	0.81[ASN][1000 genomes]
rs676683	0.85[CHB][hapmap];0.80[CHD][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs678285	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs679303	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs688176	0.80[CHB][hapmap]
rs689308	0.91[ASN][1000 genomes]
rs694058	1.00[ASN][1000 genomes]
rs694903	0.86[ASN][1000 genomes]
rs707991	0.80[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs7166	0.91[ASN][1000 genomes]
rs7744628	0.85[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs7757606	0.91[ASN][1000 genomes]
rs853416	0.85[CHB][hapmap];0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs853417	0.91[ASN][1000 genomes]
rs853418	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9328220	0.94[JPT][hapmap];0.91[ASN][1000 genomes]
rs9405219	0.84[ASN][1000 genomes]
rs9405701	1.00[ASN][1000 genomes]
rs942475	0.80[CHB][hapmap]

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	nsv532020	chr6:3417520-4140257	Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1022968	chr6:3862744-4272502	Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv538106	chr6:3862744-4272502	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats 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 target site	56 gene(s)	inside rSNPs	diseases
4	nsv1030104	chr6:4062894-4240269	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	esv2422231	chr6:4100333-4233454	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription 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	23 gene(s)	inside rSNPs	diseases
6	esv2422457	chr6:4100333-4377396	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs582008	FOXF2	cis	cerebellum	SCAN
rs582008	HUS1B	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4101800-4110200	Weak transcription	Stomach Mucosa	stomach
2	chr6:4102600-4113800	Weak transcription	Psoas Muscle	Psoas
3	chr6:4103000-4104600	Enhancers	Pancreas	Pancrea
4	chr6:4103000-4104600	Enhancers	Rectal Mucosa Donor 31	rectum
5	chr6:4103200-4104600	Enhancers	Fetal Brain Female	brain
6	chr6:4103400-4109800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr6:4103400-4110000	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr6:4103400-4115400	Weak transcription	Fetal Brain Male	brain
9	chr6:4103400-4115600	Weak transcription	Fetal Stomach	stomach
10	chr6:4103400-4115600	Weak transcription	Gastric	stomach
11	chr6:4103800-4105000	Enhancers	HepG2	liver
12	chr6:4103800-4108400	Weak transcription	Fetal Intestine Small	intestine
13	chr6:4104000-4104600	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr6:4104000-4104800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr6:4104000-4104800	Enhancers	HMEC	breast
16	chr6:4104000-4104800	Enhancers	NHEK	skin
17	chr6:4104200-4104600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr6:4104200-4105000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:4104400-4108400	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr6:4104400-4109200	Weak transcription	Skeletal Muscle Male	skeletal muscle

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