Variant report

Variant	rs7165610
Chromosome Location	chr15:73374466-73374467
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:73088811..73089611-chr15:73374330..73375082,2	MCF-7	breast:
2	chr15:73074981..73077571-chr15:73371548..73374920,3	MCF-7	breast:
3	chr15:73087557..73089460-chr15:73373408..73375516,2	MCF-7	breast:
4	chr15:73344322..73346287-chr15:73373187..73375620,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159322	Chromatin interaction
ENSG00000067141	Chromatin interaction
ENSG00000260898	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1023924	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1038137	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10467948	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11072403	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12050774	0.80[ASN][1000 genomes]
rs13379875	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1479340	0.81[EUR][1000 genomes]
rs17829836	0.80[EUR][1000 genomes]
rs2127277	0.80[EUR][1000 genomes]
rs2169951	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2899784	0.81[EUR][1000 genomes]
rs4132536	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4545783	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4609810	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4776624	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4776625	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4777590	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55836604	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55916847	0.88[EUR][1000 genomes]
rs55925663	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56269104	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56377702	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58060856	0.81[EUR][1000 genomes]
rs62016795	0.84[EUR][1000 genomes]
rs62016796	0.82[EUR][1000 genomes]
rs62016797	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62016803	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62016805	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62016806	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62016809	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62016811	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62016814	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62016849	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62016851	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7172021	0.81[EUR][1000 genomes]
rs7172396	0.81[EUR][1000 genomes]
rs8026121	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9972347	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3352103	chr15:73191535-73454001	Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv482421	chr15:73279141-73426897	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
3	nsv904338	chr15:73313691-73483718	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv517966	chr15:73349633-73488753	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv525462	chr15:73349633-73563495	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7165610	NEO1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73368200-73375600	Enhancers	Brain Substantia Nigra	brain
2	chr15:73368200-73381000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr15:73368600-73375200	Weak transcription	Aorta	Aorta
4	chr15:73369200-73374600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr15:73370200-73375600	Enhancers	Stomach Mucosa	stomach
6	chr15:73371000-73375200	Weak transcription	Gastric	stomach
7	chr15:73371000-73376600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr15:73371200-73376800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr15:73371200-73388600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr15:73371200-73397000	Weak transcription	Pancreas	Pancrea
11	chr15:73371400-73375200	Weak transcription	A549	lung
12	chr15:73371600-73377400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr15:73371600-73393800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr15:73371800-73375000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr15:73371800-73375200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr15:73372200-73375200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr15:73372400-73375000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr15:73372400-73375200	Enhancers	Duodenum Smooth Muscle	Duodenum
19	chr15:73372600-73375000	Weak transcription	Liver	Liver
20	chr15:73372600-73375200	Weak transcription	Fetal Lung	lung
21	chr15:73372600-73375400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr15:73372800-73375200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr15:73373200-73374600	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr15:73373200-73375000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr15:73373200-73375000	Weak transcription	Brain Anterior Caudate	brain
26	chr15:73373200-73375200	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr15:73373200-73375200	Weak transcription	Psoas Muscle	Psoas
28	chr15:73373200-73375400	Weak transcription	Small Intestine	intestine
29	chr15:73373800-73375000	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr15:73373800-73376200	Enhancers	Fetal Intestine Large	intestine
31	chr15:73374000-73374600	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr15:73374000-73375200	Weak transcription	Brain Angular Gyrus	brain
33	chr15:73374000-73376000	Enhancers	Duodenum Mucosa	Duodenum
34	chr15:73374200-73375200	Weak transcription	Brain Hippocampus Middle	brain
35	chr15:73374200-73375200	Weak transcription	Fetal Kidney	kidney
36	chr15:73374200-73393600	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr15:73374400-73374600	Enhancers	Fetal Intestine Small	intestine
38	chr15:73374400-73374800	Weak transcription	Brain Cingulate Gyrus	brain

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