Variant report

Variant	rs804828
Chromosome Location	chr6:37608014-37608015
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:37465289..37468195-chr6:37607347..37609837,2	K562	blood:
2	chr6:37606812..37609273-chr6:37613389..37615459,2	MCF-7	breast:
3	chr6:37601453..37608472-chr6:37609186..37615415,9	K562	blood:

Variant related genes	Relation type
ENSG00000112139	Chromatin interaction
ENSG00000198937	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10485031	1.00[CHB][hapmap]
rs10755699	0.80[CEU][hapmap];1.00[CHB][hapmap]
rs1619327	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1738454	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17639655	1.00[CHB][hapmap]
rs1776447	1.00[CHB][hapmap];0.85[LWK][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs3846877	0.80[CEU][hapmap];1.00[CHB][hapmap]
rs3887743	1.00[CHB][hapmap]
rs4236057	0.80[CEU][hapmap];1.00[CHB][hapmap]
rs6911875	0.80[CEU][hapmap];1.00[CHB][hapmap]
rs6915583	1.00[CHB][hapmap]
rs6922589	0.80[CEU][hapmap];1.00[CHB][hapmap]
rs804840	1.00[CHB][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs804841	1.00[CHB][hapmap];0.82[MEX][hapmap];1.00[ASN][1000 genomes]
rs9380696	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752124	chr6:37416219-37680622	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers 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
3	nsv1024016	chr6:37567651-37981590	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs804828	KIF6	cis	parietal	SCAN
rs804828	FGD2	cis	parietal	SCAN
rs804828	RPL10A	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37594000-37615400	Weak transcription	Fetal Brain Female	brain
2	chr6:37599200-37615600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr6:37599200-37621800	Weak transcription	NHLF	lung
4	chr6:37600400-37611400	Weak transcription	Primary B cells from peripheral blood	blood
5	chr6:37602200-37616600	Weak transcription	Right Atrium	heart
6	chr6:37602600-37610000	Weak transcription	Stomach Smooth Muscle	stomach
7	chr6:37602800-37616400	Weak transcription	Ovary	ovary
8	chr6:37604000-37610000	Weak transcription	Fetal Brain Male	brain
9	chr6:37604000-37611800	Weak transcription	Brain Germinal Matrix	brain
10	chr6:37604200-37614600	Strong transcription	Fetal Stomach	stomach
11	chr6:37604400-37611600	Weak transcription	Small Intestine	intestine
12	chr6:37605000-37611600	Weak transcription	Gastric	stomach
13	chr6:37605400-37609000	Weak transcription	Spleen	Spleen
14	chr6:37606200-37609200	Enhancers	Esophagus	oesophagus
15	chr6:37606800-37611800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr6:37606800-37615600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr6:37607000-37608600	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr6:37607000-37611600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr6:37607000-37611800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr6:37607200-37611200	Weak transcription	A549	lung
21	chr6:37607200-37611400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr6:37607400-37610600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr6:37607400-37611600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr6:37607400-37611600	Weak transcription	HMEC	breast
25	chr6:37607600-37611400	Weak transcription	Hela-S3	cervix
26	chr6:37608000-37609200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr6:37608000-37610400	Weak transcription	K562	blood

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