Variant report

Variant	rs7119
Chromosome Location	chr15:77777632-77777633
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HMG20A-6	chr15:77774392-77777949	NONHSAT047442
2	lnc-PEAK1.1-5	chr15:77777399-77777941	NONHSAT047445

Extended variants
information (count: 55 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1005752	0.83[YRI][hapmap]
rs10152181	0.81[AFR][1000 genomes]
rs1022172	0.88[AFR][1000 genomes]
rs10519167	0.92[JPT][hapmap];0.82[TSI][hapmap]
rs11072653	0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs11632729	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs11639293	0.83[JPT][hapmap]
rs11852471	0.81[AFR][1000 genomes]
rs11858641	0.96[YRI][hapmap]
rs12324627	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs12898370	0.83[JPT][hapmap]
rs12898656	0.84[JPT][hapmap]
rs12901503	0.83[YRI][hapmap]
rs12902896	0.84[JPT][hapmap]
rs12904938	0.86[AFR][1000 genomes]
rs12910361	0.88[AFR][1000 genomes]
rs12910951	0.84[JPT][hapmap]
rs12911371	0.83[AFR][1000 genomes]
rs12911649	0.92[JPT][hapmap]
rs12911963	0.83[JPT][hapmap]
rs12912050	0.83[AFR][1000 genomes]
rs12914345	0.81[AFR][1000 genomes]
rs12916682	0.84[JPT][hapmap]
rs12916973	0.84[JPT][hapmap]
rs1389436	0.81[AFR][1000 genomes]
rs1473922	0.96[YRI][hapmap]
rs1565756	0.80[YRI][hapmap]
rs1602925	0.83[AFR][1000 genomes]
rs16968835	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2055901	0.95[LWK][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs34591043	0.95[LWK][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs4886515	0.83[AFR][1000 genomes]
rs4886866	0.96[YRI][hapmap];0.80[AFR][1000 genomes]
rs62007299	0.86[AFR][1000 genomes]
rs6495240	0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs7166927	0.81[AFR][1000 genomes]
rs7175674	0.81[AFR][1000 genomes]
rs7176302	0.81[AFR][1000 genomes]
rs7178572	0.95[LWK][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs8024485	0.92[YRI][hapmap];0.86[AFR][1000 genomes]
rs8032071	0.92[JPT][hapmap];0.82[TSI][hapmap]
rs8034133	0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs8037561	0.81[AFR][1000 genomes]
rs8040318	0.84[JPT][hapmap]
rs8040702	0.84[JPT][hapmap]
rs8042307	0.84[JPT][hapmap]
rs952471	0.88[AFR][1000 genomes]
rs952472	0.88[AFR][1000 genomes]
rs965480	0.88[AFR][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

Variant related diseases (count:1)

Disease	PMID	Source
Type 2 diabetes	21490949	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7119	STRA6	cis	cerebellum	SCAN
rs7119	HMG20A	cis	parietal	SCAN
rs7119	HMG20A	cis	cerebellum	SCAN

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	chr15:77755400-77777800	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr15:77756200-77778400	Strong transcription	Fetal Thymus	thymus
8	chr15:77769400-77777800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr15:77769400-77777800	Strong transcription	HepG2	liver
10	chr15:77769400-77778000	Strong transcription	Dnd41	blood
11	chr15:77769400-77779800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr15:77769600-77778000	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr15:77769600-77778600	Strong transcription	Liver	Liver
14	chr15:77769800-77777800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr15:77769800-77777800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr15:77769800-77778000	Strong transcription	Primary T cells from cord blood	blood
17	chr15:77770000-77789200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr15:77772400-77782800	Weak transcription	Small Intestine	intestine
19	chr15:77773000-77777800	Strong transcription	Primary B cells from cord blood	blood
20	chr15:77773800-77779400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr15:77773800-77779800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr15:77774400-77779600	Weak transcription	Stomach Mucosa	stomach
23	chr15:77775000-77777800	Strong transcription	Brain Cingulate Gyrus	brain
24	chr15:77775200-77777800	Strong transcription	Brain Anterior Caudate	brain
25	chr15:77775200-77777800	Strong transcription	Brain Hippocampus Middle	brain
26	chr15:77775200-77778200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr15:77775400-77777800	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr15:77775400-77778200	Strong transcription	Esophagus	oesophagus
29	chr15:77775400-77778200	Strong transcription	Fetal Muscle Trunk	muscle
30	chr15:77775800-77777800	Strong transcription	Brain Inferior Temporal Lobe	brain
31	chr15:77775800-77779200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr15:77775800-77779600	Strong transcription	Fetal Intestine Small	intestine
33	chr15:77776000-77777800	Strong transcription	Fetal Lung	lung
34	chr15:77776000-77777800	Strong transcription	Placenta	Placenta
35	chr15:77776000-77779000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr15:77776000-77779000	Weak transcription	HMEC	breast
37	chr15:77776000-77779600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr15:77776200-77777800	Strong transcription	A549	lung
39	chr15:77776200-77778000	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr15:77776200-77779000	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr15:77776200-77779000	Weak transcription	Fetal Kidney	kidney
42	chr15:77776200-77779000	Weak transcription	Psoas Muscle	Psoas
43	chr15:77776200-77779000	Weak transcription	Right Atrium	heart
44	chr15:77776200-77779200	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr15:77776200-77779200	Weak transcription	Right Ventricle	heart
46	chr15:77776200-77787600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr15:77776200-77788200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr15:77776200-77789000	Weak transcription	Colonic Mucosa	Colon
49	chr15:77776400-77777800	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr15:77776400-77777800	Genic enhancers	iPS-20b Cell Line	embryonic stem cell

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