Variant report

Variant	rs9959071
Chromosome Location	chr18:6732846-6732847
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:6685044..6687268-chr18:6731388..6733678,2	K562	blood:
2	chr18:6543479..6544036-chr18:6732819..6733527,2	MCF-7	breast:
3	chr18:6731530..6734164-chr18:6740298..6742070,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11872330	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11873962	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11874464	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12958328	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28422970	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28581492	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28758391	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34136398	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35135219	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35421357	0.88[ASN][1000 genomes]
rs60027722	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62082767	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7229906	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7232107	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73380708	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8091694	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8092101	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8092235	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059678	chr18:6155114-6838290	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv916883	chr18:6299209-7244642	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv1055148	chr18:6527292-6790869	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv543629	chr18:6527292-6790869	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv3529901	chr18:6537233-6851509	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	esv3529902	chr18:6537233-6851509	Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv1063762	chr18:6542534-7382339	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv543630	chr18:6542534-7382339	Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv1057885	chr18:6598684-6754548	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv1060757	chr18:6682974-7051982	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
11	nsv543631	chr18:6682974-7051982	Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9959071	MYL12B	cis	parietal	SCAN
rs9959071	ARHGAP28	cis	parietal	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:6730200-6735600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr18:6730200-6747800	Weak transcription	Left Ventricle	heart
3	chr18:6730400-6735600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr18:6730800-6733000	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr18:6730800-6733000	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr18:6730800-6733800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr18:6730800-6734800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr18:6730800-6738800	Weak transcription	Stomach Smooth Muscle	stomach
9	chr18:6730800-6740400	Weak transcription	Psoas Muscle	Psoas
10	chr18:6730800-6740800	Weak transcription	Right Atrium	heart
11	chr18:6731200-6733200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr18:6731200-6735600	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr18:6731600-6733000	Enhancers	Adipose Nuclei	Adipose
14	chr18:6731600-6735400	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr18:6731600-6735600	Weak transcription	Fetal Kidney	kidney
16	chr18:6731600-6741000	Weak transcription	K562	blood
17	chr18:6731800-6733000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr18:6731800-6733000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr18:6731800-6733000	Enhancers	HUVEC	blood vessel
20	chr18:6731800-6733200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr18:6731800-6733200	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr18:6731800-6733800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr18:6731800-6733800	Active TSS	Fetal Lung	lung
24	chr18:6731800-6734600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr18:6731800-6736000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr18:6731800-6737600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr18:6731800-6738000	Weak transcription	HMEC	breast
28	chr18:6731800-6739800	Weak transcription	Placenta	Placenta
29	chr18:6731800-6743800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr18:6732000-6733000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr18:6732000-6733000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr18:6732000-6733000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr18:6732000-6733800	Weak transcription	Fetal Brain Male	brain
34	chr18:6732000-6735800	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr18:6732000-6737600	Weak transcription	HSMMtube	muscle
36	chr18:6732000-6740200	Weak transcription	NHLF	lung
37	chr18:6732200-6733800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr18:6732200-6737600	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr18:6732400-6734600	Weak transcription	Fetal Stomach	stomach
40	chr18:6732400-6734800	Weak transcription	Brain Germinal Matrix	brain
41	chr18:6732400-6737600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr18:6732400-6737600	Weak transcription	HSMM	muscle
43	chr18:6732400-6740600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr18:6732600-6735200	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr18:6732600-6735600	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr18:6732600-6740000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr18:6732800-6733800	Weak transcription	Ovary	ovary
48	chr18:6732800-6737200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr18:6732800-6737600	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr18:6732800-6740200	Weak transcription	Fetal Muscle Leg	muscle

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