Variant report

Variant	rs16896467
Chromosome Location	chr8:98972117-98972118
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:57915257..57916823-chr8:98971519..98974188,2	MCF-7	breast:
2	chr8:98964671..98967862-chr8:98969521..98972694,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000062716	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10090458	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs11994638	0.91[EUR][1000 genomes]
rs12375372	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12674810	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12675146	0.85[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12675608	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12680911	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1378121	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs16892217	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16896429	0.86[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16896468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16896471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16896476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16896503	1.00[CEU][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16896514	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16896518	1.00[CEU][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs16896521	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16896531	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs16896564	1.00[CEU][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs16896600	1.00[CEU][hapmap];1.00[AFR][1000 genomes]
rs1869607	1.00[CEU][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1961270	0.91[EUR][1000 genomes]
rs2010014	1.00[AFR][1000 genomes]
rs2045805	1.00[AFR][1000 genomes]
rs2045807	1.00[AFR][1000 genomes]
rs2061053	1.00[CEU][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2290473	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2513844	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs34354078	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35407519	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4734381	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4735508	0.83[TSI][hapmap]
rs4735514	0.88[JPT][hapmap];0.81[EUR][1000 genomes]
rs4735516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4735519	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59704264	1.00[AFR][1000 genomes]
rs60346298	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs60580631	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6980810	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6988458	1.00[AFR][1000 genomes]
rs7010226	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7018411	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72677062	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72677068	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72677085	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72677098	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72678728	0.84[AMR][1000 genomes]
rs72678733	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72678734	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72678737	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72678752	1.00[AFR][1000 genomes]
rs72678755	1.00[AFR][1000 genomes]
rs72678761	1.00[AFR][1000 genomes]
rs72678762	1.00[AFR][1000 genomes]
rs7830701	1.00[CEU][hapmap]
rs7843262	1.00[CEU][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes]
rs930817	0.88[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032904	chr8:98756076-99476925	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv539687	chr8:98756076-99476925	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv1028055	chr8:98780445-98977746	Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv891214	chr8:98849303-98990399	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv891215	chr8:98910287-98980663	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv528695	chr8:98960813-99022009	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16896467	C8orf47	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:98956600-98973600	Weak transcription	Duodenum Mucosa	Duodenum
2	chr8:98957200-98973600	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr8:98963400-98976000	Weak transcription	Fetal Brain Male	brain
4	chr8:98963800-98975200	Weak transcription	Placenta	Placenta
5	chr8:98964800-98976400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr8:98965000-98973600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr8:98965000-98980200	Weak transcription	Liver	Liver
8	chr8:98965600-98983200	Weak transcription	NHLF	lung
9	chr8:98968000-98976200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr8:98968200-98976200	Weak transcription	Gastric	stomach
11	chr8:98968200-98993800	Weak transcription	Esophagus	oesophagus
12	chr8:98968400-98973600	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr8:98968400-98973600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr8:98969200-98979800	Weak transcription	Fetal Intestine Small	intestine
15	chr8:98969800-98982600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr8:98970000-98984800	Weak transcription	Fetal Kidney	kidney
17	chr8:98970000-98985200	Weak transcription	Brain Angular Gyrus	brain
18	chr8:98970000-98992200	Weak transcription	Brain Hippocampus Middle	brain
19	chr8:98970200-98978600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr8:98970200-98984800	Weak transcription	Brain Substantia Nigra	brain
21	chr8:98970600-98973600	Weak transcription	Fetal Muscle Trunk	muscle
22	chr8:98970800-98973600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr8:98970800-98977200	Weak transcription	Colonic Mucosa	Colon
24	chr8:98971000-98973400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr8:98971000-98973800	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr8:98971200-98973600	Weak transcription	Ovary	ovary
27	chr8:98971200-98976200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr8:98971200-98982400	Weak transcription	Left Ventricle	heart
29	chr8:98971400-98973600	Weak transcription	Fetal Stomach	stomach
30	chr8:98971400-98976000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr8:98971400-98982000	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr8:98971600-98973600	Weak transcription	Fetal Muscle Leg	muscle
33	chr8:98971600-98974800	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr8:98971600-98980200	Weak transcription	Adipose Nuclei	Adipose

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