Variant report

Variant	rs1678984
Chromosome Location	chr15:42616332-42616333
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM87A-2	chr15:42615533-42616353	ucscGeneNc_uc001ztu_2

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10775126	0.94[ASN][1000 genomes]
rs10851407	0.92[ASN][1000 genomes]
rs10851408	0.92[ASN][1000 genomes]
rs10851409	0.94[ASN][1000 genomes]
rs11070370	0.94[ASN][1000 genomes]
rs11631917	0.94[ASN][1000 genomes]
rs11631983	0.94[ASN][1000 genomes]
rs11638784	0.94[ASN][1000 genomes]
rs12438509	0.87[AMR][1000 genomes]
rs12438562	0.94[ASN][1000 genomes]
rs12441700	0.92[ASN][1000 genomes]
rs12917101	0.94[ASN][1000 genomes]
rs1359003	0.94[ASN][1000 genomes]
rs1359004	0.92[ASN][1000 genomes]
rs1659212	0.97[ASN][1000 genomes]
rs1659213	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1659217	0.97[ASN][1000 genomes]
rs1659218	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1659219	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1659221	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1659222	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1678992	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1678993	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16972887	0.81[AMR][1000 genomes]
rs16973008	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16973045	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16973060	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2289295	0.97[ASN][1000 genomes]
rs2412682	0.94[ASN][1000 genomes]
rs2412685	0.94[ASN][1000 genomes]
rs2412705	0.94[ASN][1000 genomes]
rs2918459	0.97[ASN][1000 genomes]
rs2918460	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2918461	0.97[ASN][1000 genomes]
rs3743005	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3743006	0.94[ASN][1000 genomes]
rs3743007	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3743008	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3825785	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3850774	0.94[ASN][1000 genomes]
rs4329897	0.94[ASN][1000 genomes]
rs4506867	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4923940	0.94[ASN][1000 genomes]
rs4923943	0.94[ASN][1000 genomes]
rs4923945	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4924644	0.83[AMR][1000 genomes]
rs4924645	0.94[ASN][1000 genomes]
rs4924648	0.94[ASN][1000 genomes]
rs4924653	0.92[ASN][1000 genomes]
rs4924658	0.94[ASN][1000 genomes]
rs4924660	0.94[ASN][1000 genomes]
rs4924672	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4924673	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55882551	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56670003	0.87[AMR][1000 genomes]
rs56987883	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57347762	0.91[ASN][1000 genomes]
rs57393446	0.84[AMR][1000 genomes]
rs57973092	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58292736	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58712370	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59094161	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59320762	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59974698	0.89[AMR][1000 genomes]
rs61133768	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6493027	0.94[ASN][1000 genomes]
rs6493045	0.88[ASN][1000 genomes]
rs7166785	0.91[ASN][1000 genomes]
rs7168709	0.85[ASN][1000 genomes]
rs7175863	0.94[ASN][1000 genomes]
rs7177120	0.94[ASN][1000 genomes]
rs7179203	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7180279	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7181742	0.94[ASN][1000 genomes]
rs7183015	0.92[ASN][1000 genomes]
rs7183546	0.94[ASN][1000 genomes]
rs73398938	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73402707	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73407403	0.83[AMR][1000 genomes]
rs751572	0.85[ASN][1000 genomes]
rs765830	0.94[ASN][1000 genomes]
rs8024732	0.94[ASN][1000 genomes]
rs8026198	0.94[ASN][1000 genomes]
rs8031315	0.94[ASN][1000 genomes]
rs8036380	0.87[ASN][1000 genomes]
rs8036596	0.94[ASN][1000 genomes]
rs8037020	0.94[ASN][1000 genomes]
rs8041951	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9672382	0.94[ASN][1000 genomes]
rs9920921	0.94[ASN][1000 genomes]

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	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv904133	chr15:42528982-42681057	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
6	nsv832986	chr15:42587825-42753664	Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42567200-42623600	Weak transcription	Fetal Brain Male	brain
2	chr15:42568400-42656000	Weak transcription	Small Intestine	intestine
3	chr15:42568600-42630800	Weak transcription	Dnd41	blood
4	chr15:42573400-42635800	Weak transcription	Gastric	stomach
5	chr15:42576400-42620800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:42585400-42623600	Weak transcription	Colon Smooth Muscle	Colon
7	chr15:42596800-42625200	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr15:42597800-42621200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr15:42600400-42626400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr15:42600600-42627200	Weak transcription	Fetal Brain Female	brain
11	chr15:42601200-42636000	Weak transcription	Brain Germinal Matrix	brain
12	chr15:42603200-42618400	Weak transcription	HSMM	muscle
13	chr15:42603200-42627200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr15:42603200-42636000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr15:42603400-42617600	Weak transcription	Placenta	Placenta
16	chr15:42603400-42618400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr15:42603400-42619200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr15:42603400-42619200	Weak transcription	Rectal Smooth Muscle	rectum
19	chr15:42603400-42622400	Weak transcription	Fetal Heart	heart
20	chr15:42603400-42623200	Weak transcription	Brain Angular Gyrus	brain
21	chr15:42603400-42648600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr15:42603400-42648600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr15:42604000-42639400	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr15:42604200-42617800	Weak transcription	Brain Hippocampus Middle	brain
25	chr15:42604400-42618400	Weak transcription	Brain Anterior Caudate	brain
26	chr15:42604600-42616800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr15:42604600-42651200	Weak transcription	Fetal Kidney	kidney
28	chr15:42604800-42619200	Weak transcription	NHDF-Ad	bronchial
29	chr15:42605000-42618000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr15:42606000-42620400	Weak transcription	Primary hematopoietic stem cells	blood
31	chr15:42606200-42634600	Weak transcription	Pancreas	Pancrea
32	chr15:42606400-42618000	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr15:42606600-42617600	Weak transcription	Ovary	ovary
34	chr15:42606600-42617600	Weak transcription	Stomach Smooth Muscle	stomach
35	chr15:42606600-42618000	Weak transcription	Aorta	Aorta
36	chr15:42608800-42617600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr15:42613000-42617000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr15:42613000-42622200	Strong transcription	Duodenum Mucosa	Duodenum
39	chr15:42613000-42623800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr15:42613000-42624000	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr15:42613000-42624000	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr15:42613200-42616600	Strong transcription	Primary T cells from cord blood	blood
43	chr15:42613400-42621400	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr15:42613400-42624200	Strong transcription	Primary B cells from cord blood	blood
45	chr15:42613400-42626400	Strong transcription	Primary B cells from peripheral blood	blood
46	chr15:42613600-42619800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr15:42613600-42622200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr15:42613600-42623800	Strong transcription	Adipose Nuclei	Adipose
49	chr15:42613800-42616400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr15:42613800-42616800	Strong transcription	Duodenum Smooth Muscle	Duodenum

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