Variant report

Variant	rs7838399
Chromosome Location	chr8:8457080-8457081
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	chr8:8455617..8458254-chr8:8522777..8525195,2	MCF-7	breast:

Extended variants
information (count: 118 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10503378	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10503379	0.84[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11250208	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11250209	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11250210	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11250211	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11250213	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11250214	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12541355	0.80[CHB][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12541484	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12541658	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12542803	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12543456	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12544432	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12546276	0.84[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12546296	0.84[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12547034	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12549726	0.84[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12550737	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12675017	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12675869	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12676983	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12677476	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12677677	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12679599	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12679906	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12680789	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12681936	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1522836	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1533888	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1533889	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1533890	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1533891	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1533893	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1533894	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17154252	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17154268	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17154314	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17154329	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17154369	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17154375	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17154379	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17154440	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17154478	0.84[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2030566	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2177253	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2409020	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2898082	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3081466	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35016966	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35898686	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4268132	1.00[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4364633	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4367545	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4386982	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4404922	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4427178	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4504642	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4506213	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4515552	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4840994	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4840995	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4840996	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4840997	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4840998	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4840999	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4841002	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5019821	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58059590	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60510961	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60906424	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61052104	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62492871	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62492878	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62494894	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62494895	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62494897	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62494916	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62494917	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62494918	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62494919	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62494921	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73190549	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73190579	0.91[AMR][1000 genomes]
rs73190600	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73192404	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7357587	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7464820	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7813359	0.84[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7813381	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7814697	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7814889	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7819718	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7819733	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7820321	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7824587	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7824895	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7824908	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7825087	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7834575	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7843691	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs870167	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs873323	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs940027	0.86[AMR][1000 genomes];0.87[EUR][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	nsv890331	chr8:8093240-8971100	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1025994	chr8:8108863-8580201	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv1030433	chr8:8130629-8653691	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS 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	nsv539447	chr8:8130629-8653691	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv1033463	chr8:8221922-8674333	Weak transcription Bivalent/Poised TSS Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription 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	21 gene(s)	inside rSNPs	diseases
6	nsv539451	chr8:8221922-8674333	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv1019613	chr8:8239352-8636357	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv539452	chr8:8239352-8636357	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	nsv890334	chr8:8328101-8471348	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv1019606	chr8:8353661-8736992	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
11	nsv539456	chr8:8353661-8736992	Strong transcription Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
12	nsv995047	chr8:8353662-8857913	Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
13	nsv890336	chr8:8396676-8500562	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv1016933	chr8:8432279-8624770	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7838399	GFRA2	trans	brain	seeQTL
rs7838399	DIRAS3	trans	brain	seeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:8434200-8457400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr8:8441800-8458000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr8:8451800-8457200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr8:8452000-8457200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr8:8452000-8457200	Weak transcription	Fetal Brain Female	brain
6	chr8:8452200-8458000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr8:8455800-8459800	Enhancers	HUVEC	blood vessel
8	chr8:8456000-8457400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr8:8456600-8459400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr8:8456800-8457200	Enhancers	A549	lung
11	chr8:8456800-8457200	Enhancers	Hela-S3	cervix
12	chr8:8456800-8457400	Enhancers	HepG2	liver
13	chr8:8456800-8457400	Enhancers	NH-A	brain
14	chr8:8456800-8457400	Enhancers	Osteobl	bone
15	chr8:8456800-8459400	Enhancers	Liver	Liver
16	chr8:8456800-8459400	Enhancers	Placenta	Placenta
17	chr8:8456800-8459600	Enhancers	HSMM	muscle
18	chr8:8457000-8457200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr8:8457000-8457200	Enhancers	HSMMtube	muscle
20	chr8:8457000-8457400	Enhancers	Adipose Nuclei	Adipose
21	chr8:8457000-8457600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr8:8457000-8457800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr8:8457000-8457800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr8:8457000-8458000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr8:8457000-8458000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr8:8457000-8459000	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr8:8457000-8459000	Enhancers	Brain Hippocampus Middle	brain
28	chr8:8457000-8459600	Enhancers	Fetal Intestine Small	intestine
29	chr8:8457000-8460000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr8:8457000-8460400	Enhancers	Ovary	ovary

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