Variant report

Variant	rs6903060
Chromosome Location	chr6:38374397-38374398
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	chr6:38357729..38359260-chr6:38373840..38376265,2	MCF-7	breast:

Extended variants
information (count: 66 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1983605	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2294739	0.85[EUR][1000 genomes]
rs4140443	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4711538	0.85[EUR][1000 genomes]
rs4711540	0.83[EUR][1000 genomes]
rs4711541	0.93[EUR][1000 genomes]
rs4711543	0.85[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4711544	1.00[CEU][hapmap];0.91[GIH][hapmap];0.87[LWK][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs4711546	0.94[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4714151	0.84[EUR][1000 genomes]
rs4714152	0.83[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4714153	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs4714155	1.00[CEU][hapmap];0.83[YRI][hapmap];0.95[EUR][1000 genomes]
rs4714156	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.91[LWK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs4714157	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4714158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58424668	0.83[EUR][1000 genomes]
rs58807047	0.83[EUR][1000 genomes]
rs6903611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6903767	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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6923701	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs742515	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7743023	0.95[EUR][1000 genomes]
rs7748599	0.94[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7749685	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7756267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7759078	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.89[LWK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs7759629	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7764502	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7766214	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9296248	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9296249	1.00[CEU][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes]
rs9349076	0.92[EUR][1000 genomes]
rs9349077	0.94[CEU][hapmap];0.95[EUR][1000 genomes]
rs9349078	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9349079	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9357269	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9357270	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9357271	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9357272	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9366957	0.81[EUR][1000 genomes]
rs9366959	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs9366960	0.84[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs9369055	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.89[LWK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs9369057	0.94[CEU][hapmap];0.95[EUR][1000 genomes]
rs9380740	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs9380741	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.89[LWK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs9380742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9380743	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9380745	0.94[CEU][hapmap];0.83[EUR][1000 genomes]
rs9380747	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9394493	1.00[CEU][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs9394494	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.89[LWK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs9470865	0.81[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs9470867	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9470868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9470874	0.87[AFR][1000 genomes];0.94[EUR][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	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv885818	chr6:38147745-38436317	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv885820	chr6:38166511-38468887	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv602957	chr6:38305770-38395874	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1032358	chr6:38323745-38415855	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv1022724	chr6:38332368-38454527	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv602958	chr6:38362024-38446634	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6903060	MDFI	cis	parietal	SCAN
rs6903060	STK38	cis	cerebellum	SCAN
rs6903060	GLO1	cis	parietal	SCAN
rs6903060	TDRG1	cis	cerebellum	SCAN
rs6903060	PACSIN1	cis	cerebellum	SCAN
rs6903060	KCNK5	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38354000-38376000	Weak transcription	Primary T cells from cord blood	blood
2	chr6:38370800-38375200	Enhancers	Fetal Brain Male	brain
3	chr6:38371200-38375600	Enhancers	Adipose Nuclei	Adipose
4	chr6:38371600-38376400	Enhancers	Liver	Liver
5	chr6:38372000-38374800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:38372400-38374600	Weak transcription	Ovary	ovary
7	chr6:38372600-38375000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr6:38372800-38374600	Weak transcription	Primary B cells from peripheral blood	blood
9	chr6:38372800-38376200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr6:38373000-38376800	Weak transcription	Aorta	Aorta
11	chr6:38373200-38374600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr6:38373200-38374600	Weak transcription	Psoas Muscle	Psoas
13	chr6:38373200-38395600	Weak transcription	Fetal Intestine Small	intestine
14	chr6:38373800-38375200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr6:38373800-38383400	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr6:38374000-38375200	Weak transcription	Brain Hippocampus Middle	brain
17	chr6:38374000-38375200	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr6:38374200-38374400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr6:38374200-38383000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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