Variant report

Variant	rs1592641
Chromosome Location	chr18:12647240-12647241
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	chr18:12639049..12640550-chr18:12644978..12647859,2	MCF-7	breast:
2	chr18:12646496..12648953-chr18:12649691..12651231,2	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1105122	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11660232	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11663289	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11663668	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11664013	1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11664219	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11664431	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11665415	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11665542	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17595746	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1940973	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2186906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28527375	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28565322	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28575715	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28663159	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28801690	0.83[EUR][1000 genomes]
rs28815517	0.82[EUR][1000 genomes]
rs28821540	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs71351500	0.87[ASN][1000 genomes]
rs9946557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9953831	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9959145	0.83[CEU][hapmap];0.95[GIH][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9959201	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9960604	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9963755	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9966118	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9967026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs9989546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063125	chr18:12046892-12918251	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	130 gene(s)	inside rSNPs	diseases
2	nsv491873	chr18:12159445-12739784	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
3	esv3528039	chr18:12396582-12851293	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	esv3528041	chr18:12396641-12851245	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS 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	36 gene(s)	inside rSNPs	diseases
5	nsv523743	chr18:12474505-12742809	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv1820040	chr18:12635601-12725236	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	esv1817845	chr18:12635601-12733705	Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	esv1821625	chr18:12635601-12733705	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	esv1791969	chr18:12643193-12697711	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1592641	RNMT	cis	cerebellum	SCAN
rs1592641	SLMO1	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:12607800-12651800	Weak transcription	Brain Germinal Matrix	brain
2	chr18:12631200-12647800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr18:12633600-12655800	Weak transcription	Fetal Stomach	stomach
4	chr18:12637800-12652000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr18:12640400-12652000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr18:12641000-12648200	Weak transcription	Hela-S3	cervix
7	chr18:12643600-12651800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr18:12643800-12653000	Weak transcription	A549	lung
9	chr18:12644400-12651800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr18:12645800-12648600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr18:12645800-12649200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr18:12646000-12647400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr18:12646000-12647600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr18:12646000-12652200	Weak transcription	NH-A	brain
15	chr18:12646000-12653000	Weak transcription	Thymus	Thymus
16	chr18:12646000-12654000	Weak transcription	Fetal Muscle Trunk	muscle
17	chr18:12646200-12647400	Weak transcription	Fetal Muscle Leg	muscle
18	chr18:12646200-12647600	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr18:12646200-12647600	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr18:12646200-12647600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr18:12646200-12647600	Weak transcription	Osteobl	bone
22	chr18:12646200-12648200	Weak transcription	HUVEC	blood vessel
23	chr18:12646200-12648400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr18:12646200-12648400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr18:12646200-12651000	Weak transcription	Brain Substantia Nigra	brain
26	chr18:12646200-12651600	Weak transcription	HSMM	muscle
27	chr18:12646200-12651600	Weak transcription	HSMMtube	muscle
28	chr18:12646200-12651800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr18:12646200-12651800	Weak transcription	Fetal Kidney	kidney
30	chr18:12646200-12652600	Weak transcription	HMEC	breast
31	chr18:12646200-12652800	Weak transcription	Brain Anterior Caudate	brain
32	chr18:12646200-12652800	Weak transcription	K562	blood
33	chr18:12646200-12653000	Weak transcription	Right Atrium	heart
34	chr18:12646200-12653000	Weak transcription	Stomach Smooth Muscle	stomach
35	chr18:12646200-12653000	Weak transcription	NHLF	lung
36	chr18:12646200-12657000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr18:12646200-12657000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr18:12646400-12647400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr18:12646400-12647400	Weak transcription	Left Ventricle	heart
40	chr18:12646400-12647600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr18:12646400-12647600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr18:12646400-12647800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr18:12646400-12651000	Weak transcription	NHDF-Ad	bronchial
44	chr18:12646400-12651800	Weak transcription	Brain Hippocampus Middle	brain
45	chr18:12646400-12652000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr18:12646400-12652000	Weak transcription	Fetal Intestine Small	intestine
47	chr18:12646400-12652200	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr18:12646400-12652400	Weak transcription	Brain Angular Gyrus	brain
49	chr18:12646400-12652800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr18:12646400-12652800	Weak transcription	Ovary	ovary

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