Variant report

Variant	rs17585396
Chromosome Location	chr4:166144008-166144009
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MSMO1-1	chr4:166143201-166144207	NONHSAT099102

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10213277	0.87[CEU][hapmap];0.92[EUR][1000 genomes]
rs10517833	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11725167	0.84[CEU][hapmap];0.84[GIH][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs11726415	1.00[CHB][hapmap]
rs12108446	0.92[EUR][1000 genomes]
rs1530043	1.00[CHB][hapmap]
rs17046216	1.00[CHB][hapmap]
rs17488289	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17488436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17488534	1.00[CHB][hapmap]
rs17488569	1.00[CHB][hapmap]
rs17488814	0.89[ASN][1000 genomes]
rs17488835	0.89[ASN][1000 genomes]
rs17488877	0.89[ASN][1000 genomes]
rs17585515	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[EUR][1000 genomes]
rs17585550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1818471	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1986031	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28472332	0.85[EUR][1000 genomes]
rs28678592	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs36230153	0.89[ASN][1000 genomes]
rs3901486	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4588420	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs55648903	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55650232	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55806488	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56022310	1.00[ASN][1000 genomes]
rs56058696	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56104713	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56144732	0.83[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56287687	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56326646	1.00[ASN][1000 genomes]
rs56370618	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs56387271	0.89[ASN][1000 genomes]
rs56407727	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56410965	0.83[AFR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57162477	1.00[ASN][1000 genomes]
rs58426709	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58781490	0.85[EUR][1000 genomes]
rs6831119	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6853219	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72699595	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72699598	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72701606	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72701608	1.00[ASN][1000 genomes]
rs72701616	0.88[EUR][1000 genomes]
rs72701655	0.89[ASN][1000 genomes]
rs72701660	0.89[ASN][1000 genomes]
rs72701663	0.89[ASN][1000 genomes]
rs7676311	0.84[EUR][1000 genomes]
rs7680096	1.00[CHD][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	nsv1022210	chr4:165792630-166251612	Genic enhancers Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv537337	chr4:165792630-166251612	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv1021905	chr4:165852926-166212878	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv533191	chr4:165879671-166171638	Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv881168	chr4:165975122-166196438	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv980271	chr4:166140782-166154486	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17585396	TLL1	cis	parietal	SCAN
rs17585396	NAF1	cis	parietal	SCAN
rs17585396	KLHL2	cis	Artery Tibial	GTEx

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:166129600-166154400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr4:166129600-166196800	Weak transcription	Pancreas	Pancrea
3	chr4:166130200-166150800	Weak transcription	Fetal Intestine Large	intestine
4	chr4:166130400-166176800	Weak transcription	Fetal Intestine Small	intestine
5	chr4:166130600-166146200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr4:166130600-166200800	Weak transcription	Lung	lung
7	chr4:166131400-166148600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:166131600-166162800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr4:166131600-166165800	Weak transcription	Gastric	stomach
10	chr4:166131600-166196800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr4:166132000-166156400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr4:166132200-166193800	Weak transcription	Fetal Brain Female	brain
13	chr4:166134000-166146000	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr4:166135800-166152600	Weak transcription	Brain Germinal Matrix	brain
15	chr4:166135800-166159000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr4:166136000-166176800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr4:166137600-166162800	Weak transcription	NH-A	brain
18	chr4:166137800-166194200	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr4:166138000-166157200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr4:166138000-166161600	Weak transcription	HSMMtube	muscle
21	chr4:166138200-166168800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr4:166138400-166185600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr4:166142400-166144200	Enhancers	HepG2	liver
24	chr4:166142400-166144400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr4:166142400-166144600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr4:166142400-166144600	Enhancers	Brain Anterior Caudate	brain
27	chr4:166142400-166144600	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr4:166142400-166144800	Enhancers	Liver	Liver
29	chr4:166142400-166144800	Enhancers	Brain Substantia Nigra	brain
30	chr4:166142400-166144800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr4:166142400-166145200	Enhancers	HMEC	breast
32	chr4:166142600-166144200	Enhancers	Muscle Satellite Cultured Cells	--
33	chr4:166142600-166144800	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr4:166142600-166144800	Enhancers	Brain Angular Gyrus	brain
35	chr4:166142600-166144800	Enhancers	Hela-S3	cervix
36	chr4:166142800-166144400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr4:166142800-166144400	Weak transcription	Right Ventricle	heart
38	chr4:166142800-166144400	Weak transcription	Spleen	Spleen
39	chr4:166142800-166165800	Weak transcription	Esophagus	oesophagus
40	chr4:166142800-166176800	Weak transcription	Duodenum Mucosa	Duodenum
41	chr4:166143000-166144200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr4:166143200-166144200	Enhancers	Primary T cells fromperipheralblood	blood
43	chr4:166143200-166144200	Enhancers	NHDF-Ad	bronchial
44	chr4:166143200-166144800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
45	chr4:166143200-166144800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr4:166143400-166144200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr4:166143400-166144200	Enhancers	Primary B cells from peripheral blood	blood
48	chr4:166143400-166144200	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr4:166143400-166144200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr4:166143400-166144200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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