Variant report

Variant	rs13015862
Chromosome Location	chr2:152195490-152195491
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:152116855..152118703-chr2:152192854..152195590,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NMI-1	chr2:152194344-152195913	ENSG00000248650
2	lnc-NMI-1	chr2:152194342-152195913	NR_110248

Variant related genes	Relation type
ENSG00000184898	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1023635	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1048135	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11678123	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11678951	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11680338	0.81[ASN][1000 genomes]
rs11683487	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11691055	0.81[ASN][1000 genomes]
rs11691217	0.81[ASN][1000 genomes]
rs11692626	0.86[EUR][1000 genomes]
rs11730	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12467046	0.81[ASN][1000 genomes]
rs12471191	0.81[ASN][1000 genomes]
rs12471886	0.92[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12476687	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12624156	0.88[ASN][1000 genomes]
rs12693004	0.88[ASN][1000 genomes]
rs12987765	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12996459	0.81[ASN][1000 genomes]
rs12999396	0.86[EUR][1000 genomes]
rs13001328	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13004590	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13018429	0.86[EUR][1000 genomes]
rs13020443	0.86[EUR][1000 genomes]
rs13020962	0.81[ASN][1000 genomes]
rs13027425	0.81[ASN][1000 genomes]
rs17798290	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2113508	0.81[EUR][1000 genomes]
rs2218880	0.80[ASN][1000 genomes]
rs2271811	0.81[ASN][1000 genomes]
rs2278090	0.87[ASN][1000 genomes]
rs34028108	0.89[ASN][1000 genomes]
rs34408744	0.86[EUR][1000 genomes]
rs34452578	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34538548	0.87[ASN][1000 genomes]
rs35659175	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35723696	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35863408	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3771882	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3845843	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3854012	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3856557	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4664322	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4664336	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4664347	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4664349	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4665114	0.81[ASN][1000 genomes]
rs4665137	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4665150	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4665168	0.88[ASN][1000 genomes]
rs55775354	0.81[ASN][1000 genomes]
rs56335263	0.88[ASN][1000 genomes]
rs56376752	0.81[ASN][1000 genomes]
rs57201382	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs66521733	0.85[ASN][1000 genomes]
rs6707889	0.86[EUR][1000 genomes]
rs6713041	0.81[EUR][1000 genomes]
rs6726634	0.86[EUR][1000 genomes]
rs6739517	0.80[ASN][1000 genomes]
rs67725431	0.88[ASN][1000 genomes]
rs68058019	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs73004003	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7349449	0.86[EUR][1000 genomes]
rs7558169	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7559296	0.80[ASN][1000 genomes]
rs7574228	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3693426	chr2:151725792-152295862	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1012891	chr2:152019809-152306897	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv1013484	chr2:152028515-152473913	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv535983	chr2:152028515-152473913	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
5	nsv1012139	chr2:152114637-152389516	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv1011339	chr2:152114637-152392940	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv999748	chr2:152135514-152476396	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13015862	TNFAIP6	cis	Whole Blood	GTEx
rs13015862	NMI	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152191200-152195600	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr2:152191400-152195600	Weak transcription	NH-A	brain
3	chr2:152191400-152195600	Weak transcription	NHLF	lung
4	chr2:152191400-152195600	Weak transcription	Osteobl	bone
5	chr2:152192200-152196000	Enhancers	Monocytes-CD14+_RO01746	blood
6	chr2:152193200-152196000	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr2:152193200-152196000	Enhancers	HUVEC	blood vessel
8	chr2:152193400-152196000	Enhancers	Muscle Satellite Cultured Cells	--
9	chr2:152194000-152195600	Weak transcription	Fetal Muscle Leg	muscle
10	chr2:152194000-152196200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:152194200-152195600	Weak transcription	Adipose Nuclei	Adipose
12	chr2:152194200-152195800	Weak transcription	Fetal Muscle Trunk	muscle
13	chr2:152194400-152195600	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr2:152194600-152195600	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr2:152194600-152196800	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr2:152194800-152196600	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr2:152194800-152196800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:152195000-152195600	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr2:152195000-152195800	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr2:152195000-152195800	Weak transcription	NHDF-Ad	bronchial
21	chr2:152195000-152196600	Enhancers	H1 Cell Line	embryonic stem cell
22	chr2:152195200-152195800	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr2:152195400-152195600	Enhancers	Brain Anterior Caudate	brain
24	chr2:152195400-152195600	Enhancers	Fetal Brain Female	brain
25	chr2:152195400-152195600	Enhancers	Fetal Lung	lung
26	chr2:152195400-152195800	Enhancers	H9 Cell Line	embryonic stem cell
27	chr2:152195400-152196000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr2:152195400-152196600	Enhancers	HUES64 Cell Line	embryonic stem cell

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