Variant report

Variant	rs2061692
Chromosome Location	chr18:9508333-9508334
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:9474567..9476576-chr18:9506542..9508351,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TWSG1-1	chr18:9506240-9509724	ENSG00000266805.1

Variant related genes	Relation type
ENSG00000017797	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10468796	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10468797	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10853380	0.86[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10898	0.86[CHB][hapmap]
rs11663979	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11664312	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12386073	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12386075	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12386078	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12454651	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12454987	1.00[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12457895	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1561997	0.95[ASN][1000 genomes]
rs1561998	0.83[CHB][hapmap]
rs16955157	0.91[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2028660	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2241943	0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs28510500	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs329006	0.83[CHB][hapmap]
rs329007	0.83[CHB][hapmap]
rs4798819	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58103465	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58651706	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59277394	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62086154	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62087367	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62087375	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7234529	0.88[ASN][1000 genomes]
rs7235585	0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7238922	0.93[ASN][1000 genomes]
rs73395727	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8092935	0.83[CHB][hapmap]

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	nsv916373	chr18:9026803-9592201	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv1056407	chr18:9144345-9553764	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv1062025	chr18:9287249-9552470	Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Enhancers Weak 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 miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv543643	chr18:9287249-9552470	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv833585	chr18:9401630-9597291	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv428005	chr18:9401658-9542396	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2061692	MPPE1	cis	parietal	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9477000-9514000	Weak transcription	NH-A	brain
2	chr18:9477200-9513800	Weak transcription	HSMM	muscle
3	chr18:9478000-9508400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr18:9478000-9522400	Weak transcription	Hela-S3	cervix
5	chr18:9479000-9514000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr18:9479000-9533200	Weak transcription	Aorta	Aorta
7	chr18:9479000-9533600	Weak transcription	Gastric	stomach
8	chr18:9480200-9513800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr18:9483000-9513800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr18:9492600-9514000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr18:9495000-9518000	Weak transcription	Liver	Liver
12	chr18:9495000-9518000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr18:9495200-9530400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr18:9495200-9533600	Weak transcription	Right Ventricle	heart
15	chr18:9495400-9512800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr18:9495400-9514000	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr18:9495400-9524000	Weak transcription	Spleen	Spleen
18	chr18:9495400-9534000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr18:9495800-9514000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr18:9495800-9517000	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr18:9496000-9513800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr18:9496800-9534000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr18:9497400-9532600	Weak transcription	Colonic Mucosa	Colon
24	chr18:9497600-9517200	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr18:9497800-9513800	Weak transcription	NHEK	skin
26	chr18:9498400-9523200	Weak transcription	Esophagus	oesophagus
27	chr18:9499400-9525000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr18:9500800-9535000	Weak transcription	Fetal Heart	heart
29	chr18:9502000-9514000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr18:9502200-9514000	Weak transcription	Dnd41	blood
31	chr18:9502200-9519800	Weak transcription	Brain Angular Gyrus	brain
32	chr18:9503000-9513600	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr18:9503000-9517200	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr18:9503600-9513800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr18:9503800-9513000	Weak transcription	Fetal Muscle Leg	muscle
36	chr18:9503800-9513600	Weak transcription	Primary T cells from cord blood	blood
37	chr18:9503800-9514000	Weak transcription	Fetal Brain Female	brain
38	chr18:9503800-9517400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr18:9504000-9512800	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr18:9504000-9513600	Weak transcription	Primary B cells from cord blood	blood
41	chr18:9504000-9515200	Weak transcription	Brain Hippocampus Middle	brain
42	chr18:9505000-9513800	Weak transcription	HepG2	liver
43	chr18:9505200-9513000	Weak transcription	Fetal Intestine Large	intestine
44	chr18:9505200-9524600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr18:9505400-9513600	Weak transcription	Primary hematopoietic stem cells	blood
46	chr18:9505600-9513600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr18:9505800-9513800	Weak transcription	Stomach Mucosa	stomach
48	chr18:9506000-9509000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr18:9506200-9508400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr18:9506200-9508400	Enhancers	Stomach Smooth Muscle	stomach

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