Variant report

Variant	rs4945826
Chromosome Location	chr6:109575070-109575071
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:18)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:109573915..109575817-chr6:109614011..109616361,2	K562	blood:
2	chr6:109573548..109576150-chr6:109616367..109617967,2	MCF-7	breast:
3	chr6:109562155..109565260-chr6:109572597..109575584,3	K562	blood:
4	chr6:109573600..109575785-chr6:109578513..109582228,5	K562	blood:
5	chr6:109571108..109577979-chr6:109701689..109707468,12	MCF-7	breast:
6	chr6:109573915..109576390-chr6:109614861..109616762,2	K562	blood:
7	chr6:109574818..109576352-chr6:109658759..109661522,2	MCF-7	breast:
8	chr6:109573090..109575242-chr6:109576098..109578266,2	K562	blood:
9	chr6:109557258..109559203-chr6:109573548..109577382,4	K562	blood:
10	chr6:109574650..109576524-chr6:109616108..109618484,2	MCF-7	breast:
11	chr6:109572844..109579013-chr6:109586013..109590515,6	MCF-7	breast:
12	chr6:109545348..109547132-chr6:109572253..109575159,2	MCF-7	breast:
13	chr6:109414191..109416076-chr6:109573130..109575129,2	MCF-7	breast:
14	chr20:52270865..52273863-chr6:109572991..109575305,2	MCF-7	breast:
15	chr6:109572724..109576435-chr6:109701396..109704510,5	MCF-7	breast:
16	chr6:109574243..109576098-chr6:109577884..109580238,2	MCF-7	breast:
17	chr6:109572927..109577072-chr6:109577808..109581744,6	MCF-7	breast:
18	chr6:109573371..109575785-chr6:109578513..109580887,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000243587	Chromatin interaction
ENSG00000203799	Chromatin interaction
ENSG00000080546	Chromatin interaction
ENSG00000260273	Chromatin interaction
ENSG00000135535	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1006081	0.82[ASW][hapmap];1.00[CEU][hapmap];0.86[GIH][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11153164	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12191774	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12201929	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12660449	0.84[CEU][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap]
rs1521905	0.82[AFR][1000 genomes]
rs2222392	0.82[AFR][1000 genomes]
rs352849	0.80[JPT][hapmap]
rs3941888	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4946949	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4946953	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4946955	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4946956	0.82[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4946957	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4946962	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62436600	0.85[ASN][1000 genomes]
rs62436601	0.85[ASN][1000 genomes]
rs6568559	0.82[AFR][1000 genomes]
rs6568560	0.82[AFR][1000 genomes]
rs6902892	1.00[LWK][hapmap]
rs6903519	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6903695	1.00[ASW][hapmap];1.00[LWK][hapmap];0.81[AFR][1000 genomes]
rs6927569	1.00[ASW][hapmap];0.90[LWK][hapmap];0.86[MKK][hapmap];0.83[AFR][1000 genomes]
rs7744284	0.83[AFR][1000 genomes]
rs7755970	1.00[ASW][hapmap];0.90[LWK][hapmap];0.88[MKK][hapmap]
rs7757193	0.84[CEU][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap]
rs7757347	0.81[AFR][1000 genomes]
rs7773815	0.83[AFR][1000 genomes]
rs7774377	0.85[AFR][1000 genomes]
rs7774390	1.00[ASW][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];0.85[AFR][1000 genomes]
rs884366	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9320282	1.00[YRI][hapmap]
rs9374083	0.84[MEX][hapmap]
rs9386797	1.00[LWK][hapmap]
rs9487053	1.00[YRI][hapmap];0.83[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527657	chr6:109533385-109579675	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4945826	FYN	cis	parietal	SCAN
rs4945826	CD164	cis	Muscle Skeletal	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109564000-109590400	Weak transcription	Psoas Muscle	Psoas
2	chr6:109572200-109578800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:109572400-109577600	Enhancers	Adipose Nuclei	Adipose
4	chr6:109572600-109577800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr6:109572800-109590400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr6:109572800-109595200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr6:109573200-109575200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:109573200-109589800	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr6:109573400-109575200	Enhancers	Colon Smooth Muscle	Colon
10	chr6:109573600-109577800	Weak transcription	A549	lung
11	chr6:109573600-109590200	Weak transcription	Gastric	stomach
12	chr6:109573800-109577200	Weak transcription	K562	blood
13	chr6:109574000-109575400	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr6:109574400-109577800	Weak transcription	Liver	Liver
15	chr6:109574400-109579400	Weak transcription	Fetal Intestine Large	intestine
16	chr6:109574600-109575400	Weak transcription	Fetal Muscle Leg	muscle
17	chr6:109574600-109576000	Enhancers	Fetal Kidney	kidney
18	chr6:109574600-109576800	Weak transcription	Fetal Intestine Small	intestine
19	chr6:109574600-109583400	Weak transcription	Placenta	Placenta
20	chr6:109574800-109577000	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr6:109574800-109578800	Weak transcription	HepG2	liver
22	chr6:109575000-109576600	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr6:109575000-109576800	Weak transcription	Stomach Mucosa	stomach

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