Variant report

Variant	rs12240685
Chromosome Location	chr10:112651120-112651121
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:112506144..112507873-chr10:112650774..112653771,2	MCF-7	breast:
2	chr10:112650461..112651966-chr10:112654927..112656997,2	MCF-7	breast:
3	chr10:112650669..112653326-chr10:112662999..112664780,3	K562	blood:
4	chr10:112631001..112634625-chr10:112648231..112651298,3	MCF-7	breast:
5	chr10:112630166..112634091-chr10:112649118..112655902,7	MCF-7	breast:
6	chr10:112650560..112652167-chr10:112657249..112659625,2	K562	blood:

Variant related genes	Relation type
ENSG00000150593	Chromatin interaction
ENSG00000214413	Chromatin interaction
ENSG00000265827	Chromatin interaction
ENSG00000203497	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10082499	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10787286	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10787291	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10787293	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10787299	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10885059	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10885060	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10885061	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10885064	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10885071	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10885076	0.87[EUR][1000 genomes]
rs11195361	0.83[AFR][1000 genomes]
rs11195366	0.91[AFR][1000 genomes]
rs11195381	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11195387	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11195390	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11195398	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12242177	0.83[EUR][1000 genomes]
rs12242928	0.83[EUR][1000 genomes]
rs12258559	0.88[AFR][1000 genomes]
rs12261765	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12776359	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12776861	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17186196	0.80[AFR][1000 genomes]
rs2146544	0.91[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs34401279	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34893229	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35394459	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35793075	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35946882	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3750619	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3763692	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4917589	0.80[ASN][1000 genomes]
rs61864641	0.80[AFR][1000 genomes]
rs6585026	0.87[EUR][1000 genomes]
rs7070962	0.81[AFR][1000 genomes]
rs7089687	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7919142	0.91[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs9663346	0.86[AFR][1000 genomes];0.83[EUR][1000 genomes]

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	nsv1045608	chr10:112524813-112677557	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1041758	chr10:112552897-112677557	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1051566	chr10:112580049-112730573	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv1035602	chr10:112636053-112781413	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv1051327	chr10:112650316-112772917	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	nsv540774	chr10:112650316-112772917	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12240685	LOC92482	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:112632800-112678000	Weak transcription	Lung	lung
2	chr10:112632800-112678200	Weak transcription	Spleen	Spleen
3	chr10:112633200-112656000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr10:112633200-112656800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr10:112633400-112662000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr10:112633600-112653800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr10:112633600-112655200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr10:112633800-112659800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr10:112634000-112655000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr10:112634000-112655800	Weak transcription	Psoas Muscle	Psoas
11	chr10:112634000-112656000	Weak transcription	Right Ventricle	heart
12	chr10:112634000-112662400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr10:112634200-112655800	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr10:112634600-112656600	Weak transcription	NHEK	skin
15	chr10:112634800-112661800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr10:112634800-112677400	Weak transcription	HUVEC	blood vessel
17	chr10:112635400-112657000	Strong transcription	HSMM	muscle
18	chr10:112635400-112661800	Strong transcription	Placenta	Placenta
19	chr10:112635600-112660600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr10:112635600-112662200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr10:112635600-112663400	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr10:112635800-112662200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr10:112636000-112652000	Strong transcription	Fetal Intestine Large	intestine
24	chr10:112636000-112664400	Strong transcription	Fetal Thymus	thymus
25	chr10:112636200-112656200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr10:112636400-112664800	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr10:112637400-112656200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr10:112639200-112661000	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr10:112641800-112655200	Weak transcription	Brain Angular Gyrus	brain
30	chr10:112642200-112655000	Weak transcription	Aorta	Aorta
31	chr10:112643000-112667200	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr10:112644000-112653200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr10:112644000-112655000	Weak transcription	Small Intestine	intestine
34	chr10:112644000-112664000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr10:112644200-112651200	Weak transcription	NHLF	lung
36	chr10:112644200-112653200	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr10:112644200-112653200	Weak transcription	Fetal Heart	heart
38	chr10:112644200-112655000	Weak transcription	Stomach Smooth Muscle	stomach
39	chr10:112644200-112655200	Strong transcription	Primary B cells from peripheral blood	blood
40	chr10:112644200-112656600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr10:112644200-112656800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr10:112644200-112656800	Weak transcription	Gastric	stomach
43	chr10:112644200-112663200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr10:112644200-112664400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr10:112644200-112678000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr10:112644800-112655200	Weak transcription	Ovary	ovary
47	chr10:112644800-112664800	Strong transcription	Primary T cells fromperipheralblood	blood
48	chr10:112644800-112675000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr10:112645000-112655000	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr10:112645000-112655600	Weak transcription	Left Ventricle	heart

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