Variant report

Variant	rs16905862
Chromosome Location	chr8:91897711-91897712
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:91888858..91893831-chr8:91896562..91901698,7	MCF-7	breast:
2	chr8:91764211..91766623-chr8:91897125..91900708,3	MCF-7	breast:
3	chr8:91895952..91898016-chr8:91960645..91963598,2	MCF-7	breast:
4	chr8:91891201..91893872-chr8:91896003..91898098,2	K562	blood:
5	chr8:91888393..91905767-chr8:91919159..91931807,48	MCF-7	breast:
6	chr8:91870161..91874296-chr8:91895687..91899910,5	MCF-7	breast:
7	chr8:91895496..91897971-chr8:91924630..91926928,4	MCF-7	breast:
8	chr8:91655658..91658801-chr8:91893915..91897797,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000254251	Chromatin interaction
ENSG00000180694	Chromatin interaction
ENSG00000246792	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10087080	1.00[CHD][hapmap]
rs10091357	1.00[CHD][hapmap]
rs10490979	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10504902	1.00[CHD][hapmap]
rs1060583	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.84[LWK][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11989738	0.92[GIH][hapmap]
rs11997330	1.00[CHD][hapmap]
rs12114104	1.00[CHD][hapmap]
rs12114679	1.00[CHD][hapmap]
rs16905427	1.00[CHD][hapmap]
rs16906071	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16907242	0.83[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.82[EUR][1000 genomes]
rs34503257	0.82[EUR][1000 genomes]
rs4260862	1.00[CHD][hapmap]
rs4645524	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56871170	0.82[EUR][1000 genomes]
rs58183914	0.82[EUR][1000 genomes]
rs58624537	0.84[ASN][1000 genomes]
rs59801655	0.86[EUR][1000 genomes]
rs60121972	0.82[EUR][1000 genomes]
rs6471263	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6651175	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap];0.82[EUR][1000 genomes]
rs6999220	0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes]
rs7006863	0.83[CEU][hapmap];1.00[CHB][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7017072	1.00[ASW][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs73295963	0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs73298014	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73299920	0.84[ASN][1000 genomes]
rs73299946	0.82[EUR][1000 genomes]
rs73299965	0.82[EUR][1000 genomes]
rs73299977	0.82[EUR][1000 genomes]
rs73299979	0.82[EUR][1000 genomes]
rs73299981	0.82[EUR][1000 genomes]
rs7818979	0.83[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.82[EUR][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	nsv1028628	chr8:91680968-92418954	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv539672	chr8:91680968-92418954	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16905862	NRGN	trans	lymphoblastoid	seeQTL
rs16905862	CCNE2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:91876800-91901000	Weak transcription	Aorta	Aorta
2	chr8:91890400-91907600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr8:91890600-91902800	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr8:91893800-91897800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr8:91895800-91899800	Weak transcription	NH-A	brain
6	chr8:91896000-91901200	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr8:91896000-91907200	Weak transcription	Stomach Smooth Muscle	stomach
8	chr8:91896000-91907600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr8:91896000-91907600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr8:91896200-91900000	Weak transcription	Liver	Liver
11	chr8:91896200-91900000	Weak transcription	NHLF	lung
12	chr8:91896200-91900400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr8:91896200-91901000	Weak transcription	Fetal Heart	heart
14	chr8:91896200-91901400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr8:91896600-91899800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr8:91896600-91900000	Weak transcription	NHDF-Ad	bronchial
17	chr8:91896800-91899800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr8:91897200-91901600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr8:91897600-91897800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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