Variant report

Variant	rs41420946
Chromosome Location	chr8:108325064-108325065
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	chr8:108324753..108329300-chr8:108347441..108349729,6	K562	blood:
2	chr8:108323328..108325135-chr8:108339439..108342402,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000154188	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10505105	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];0.95[TSI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1433195	0.80[CHD][hapmap];0.93[JPT][hapmap]
rs1433196	0.93[JPT][hapmap]
rs17295051	0.87[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17295555	0.86[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17296358	0.81[ASN][1000 genomes]
rs17296456	0.86[CHB][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs17296616	0.86[CHB][hapmap];0.80[CHD][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs17368764	0.86[CHB][hapmap];0.80[CHD][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs36036692	0.85[ASN][1000 genomes]
rs4133395	0.93[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs55748473	0.85[ASN][1000 genomes]
rs56134158	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6992940	0.81[ASN][1000 genomes]
rs7004172	0.86[CHB][hapmap];0.93[JPT][hapmap]
rs7011520	0.81[ASN][1000 genomes]
rs72672504	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72672522	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029202	chr8:107796289-108384241	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv539712	chr8:107796289-108384241	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1034210	chr8:107796489-108384102	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv539713	chr8:107796489-108384102	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv529383	chr8:107796490-108368465	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv915821	chr8:107796490-108393008	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv916496	chr8:107813722-108338822	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1028726	chr8:107816841-108392547	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv497805	chr8:107852509-108368371	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	esv2764100	chr8:108220671-108469233	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv1030831	chr8:108224295-108466437	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	nsv539714	chr8:108224295-108466437	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	nsv465760	chr8:108224687-108485912	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
14	nsv611851	chr8:108224687-108485912	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs41420946	SLC28A1	trans	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:108276600-108327600	Weak transcription	Aorta	Aorta
2	chr8:108304600-108326400	Weak transcription	Ovary	ovary
3	chr8:108314600-108326200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr8:108315200-108326200	Weak transcription	Fetal Lung	lung
5	chr8:108323000-108326400	Weak transcription	Right Atrium	heart
6	chr8:108323000-108326600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr8:108323000-108328000	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr8:108323000-108349000	Weak transcription	HSMM	muscle
9	chr8:108323200-108326200	Weak transcription	Osteobl	bone
10	chr8:108323200-108326400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr8:108323200-108327400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr8:108323400-108327000	Weak transcription	Fetal Kidney	kidney
13	chr8:108323400-108327800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr8:108324400-108325200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr8:108324400-108325200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr8:108324400-108325200	Enhancers	NHLF	lung
17	chr8:108324400-108326800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr8:108324600-108325200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr8:108324600-108325200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr8:108324600-108325200	Genic enhancers	K562	blood
21	chr8:108324600-108325400	Enhancers	Dnd41	blood
22	chr8:108324600-108326400	Enhancers	Primary hematopoietic stem cells	blood
23	chr8:108324800-108325200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr8:108324800-108325200	Enhancers	Fetal Thymus	thymus
25	chr8:108324800-108325200	Enhancers	A549	lung
26	chr8:108324800-108325200	Enhancers	NHDF-Ad	bronchial

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