Variant report

Variant	rs6458003
Chromosome Location	chr6:37556555-37556556
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:37544738..37547399-chr6:37555553..37558096,2	MCF-7	breast:
2	chr6:37556006..37559631-chr6:37561589..37564141,4	K562	blood:

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10510137	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs17574830	1.00[JPT][hapmap]
rs68147444	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6904950	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6906840	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6925202	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6932068	0.92[ASN][1000 genomes]
rs7756395	0.81[EUR][1000 genomes]
rs9462330	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9462331	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9462332	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9462333	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9470630	0.83[ASN][1000 genomes]
rs9470632	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9470633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9470640	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6458003	LRFN2	cis	parietal	SCAN
rs6458003	GLP1R	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37534200-37556600	Weak transcription	Right Atrium	heart
2	chr6:37552000-37556800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr6:37552600-37558600	Enhancers	Fetal Brain Male	brain
4	chr6:37553400-37559400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:37555000-37556600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr6:37555000-37556800	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr6:37555200-37556600	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr6:37555200-37556800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr6:37555400-37556600	Enhancers	H1 Cell Line	embryonic stem cell
10	chr6:37555400-37556600	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr6:37555400-37556800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:37555400-37556800	Enhancers	Brain Germinal Matrix	brain
13	chr6:37555600-37556600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr6:37555600-37556600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
15	chr6:37555600-37556600	Bivalent Enhancer	Fetal Muscle Leg	muscle
16	chr6:37555800-37556600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr6:37556000-37556800	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr6:37556000-37556800	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr6:37556200-37556600	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr6:37556200-37556600	Bivalent Enhancer	Adipose Nuclei	Adipose
21	chr6:37556200-37556800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr6:37556200-37556800	Enhancers	Fetal Brain Female	brain
23	chr6:37556400-37556600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr6:37556400-37556800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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