Variant report

Variant	rs952471
Chromosome Location	chr15:77776498-77776499
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PEAK1.1-2	chr15:77776140-77776947	ENSG00000244881
2	lnc-HMG20A-6	chr15:77774392-77777949	NONHSAT047442

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs1005752	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10152181	0.91[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1022172	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11072653	0.93[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11632966	0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11633054	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11636554	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11852471	0.91[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11857450	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1191196	0.93[ASN][1000 genomes]
rs12324627	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12901503	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12904938	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12905951	0.88[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs12906708	0.90[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12910361	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12910480	0.85[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs12911371	0.93[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12912050	0.93[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12914345	0.91[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1389436	0.91[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1473922	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1493700	0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1565756	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1565757	0.86[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1602925	0.93[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2055901	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34591043	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4886515	0.93[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4886858	0.90[ASN][1000 genomes]
rs4886862	0.93[ASN][1000 genomes]
rs4886866	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4886869	0.94[ASN][1000 genomes]
rs59153558	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62007299	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62009066	0.81[ASN][1000 genomes]
rs6495240	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7119	0.88[AFR][1000 genomes]
rs7166927	0.91[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7167794	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7170877	0.83[EUR][1000 genomes]
rs7171448	0.83[EUR][1000 genomes]
rs7172144	0.80[EUR][1000 genomes]
rs7175674	0.91[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7176302	0.91[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7177055	0.82[EUR][1000 genomes]
rs7178572	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8024485	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8030074	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs8034133	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8037561	0.91[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs869301	0.81[EUR][1000 genomes]
rs907388	0.83[EUR][1000 genomes]
rs952472	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs965480	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];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	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1045376	chr15:77354671-77801487	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv542443	chr15:77354671-77801487	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv916323	chr15:77485765-78121259	Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats 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
5	nsv1043284	chr15:77740632-77884026	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv570139	chr15:77762493-77865459	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77750400-77777800	Strong transcription	Primary B cells from peripheral blood	blood
2	chr15:77750600-77777800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr15:77750600-77779200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:77750600-77779600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr15:77750800-77780400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr15:77753400-77777600	Strong transcription	Rectal Mucosa Donor 31	rectum
7	chr15:77755400-77777800	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr15:77756200-77778400	Strong transcription	Fetal Thymus	thymus
9	chr15:77767200-77777400	Strong transcription	GM12878-XiMat	blood
10	chr15:77767600-77777600	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr15:77769400-77777600	Strong transcription	Primary T helper cells PMA-I stimulated	--
12	chr15:77769400-77777600	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr15:77769400-77777800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr15:77769400-77777800	Strong transcription	HepG2	liver
15	chr15:77769400-77778000	Strong transcription	Dnd41	blood
16	chr15:77769400-77779800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr15:77769600-77777600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr15:77769600-77777600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
19	chr15:77769600-77778000	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr15:77769600-77778600	Strong transcription	Liver	Liver
21	chr15:77769800-77777600	Strong transcription	Primary hematopoietic stem cells	blood
22	chr15:77769800-77777800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr15:77769800-77777800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr15:77769800-77778000	Strong transcription	Primary T cells from cord blood	blood
25	chr15:77770000-77777600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr15:77770000-77789200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr15:77770400-77777600	Strong transcription	Thymus	Thymus
28	chr15:77772400-77782800	Weak transcription	Small Intestine	intestine
29	chr15:77773000-77777800	Strong transcription	Primary B cells from cord blood	blood
30	chr15:77773400-77777600	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr15:77773800-77776600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr15:77773800-77779400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr15:77773800-77779800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
34	chr15:77774400-77777000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr15:77774400-77779600	Weak transcription	Stomach Mucosa	stomach
36	chr15:77774600-77776800	Genic enhancers	Adipose Nuclei	Adipose
37	chr15:77774800-77777000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr15:77774800-77777200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr15:77774800-77777600	Strong transcription	Fetal Brain Male	brain
40	chr15:77775000-77776600	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr15:77775000-77777600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr15:77775000-77777600	Strong transcription	Fetal Intestine Large	intestine
43	chr15:77775000-77777600	Strong transcription	K562	blood
44	chr15:77775000-77777800	Strong transcription	Brain Cingulate Gyrus	brain
45	chr15:77775200-77776800	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr15:77775200-77776800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr15:77775200-77777200	Weak transcription	Brain Angular Gyrus	brain
48	chr15:77775200-77777400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr15:77775200-77777800	Strong transcription	Brain Anterior Caudate	brain
50	chr15:77775200-77777800	Strong transcription	Brain Hippocampus Middle	brain

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