Variant report

Variant	rs880034
Chromosome Location	chr8:119633261-119633262
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC023590.1.1-2	chr8:119633240-119633425	NONHSAT128412

Extended variants
information (count: 35 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10108302	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1568484	0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2460964	1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs2460965	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2460966	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2460967	0.86[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2460968	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2460970	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2460971	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2460972	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2460973	0.81[EUR][1000 genomes]
rs2460975	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2460976	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2460979	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2460982	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2460983	0.83[ASN][1000 genomes]
rs2514576	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2514591	1.00[CHB][hapmap];0.96[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2514592	1.00[CHB][hapmap];0.96[CHD][hapmap];0.90[JPT][hapmap];0.98[ASN][1000 genomes]
rs2514593	0.98[ASN][1000 genomes]
rs2514594	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2514596	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2514600	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2514608	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2514609	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2514610	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2514611	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2514612	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3133404	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62531943	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs880033	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv891413	chr8:119607281-119679668	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	esv1814789	chr8:119627671-119672134	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv465786	chr8:119627671-119767165	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv612048	chr8:119627671-119767165	Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs880034	SAMD12	cis	Skin Sun Exposed Lower leg	GTEx
rs880034		cis	Lymphoblastoid	GTEx
rs880034	LOC377696	cis	multi-tissue	Pritchard
rs880034	SAMD12	cis	multi-tissue	Pritchard
rs880034	Hs.453941	cis	multi-tissue	Pritchard
rs880034	SAMD12	cis	Lymphoblastoid	GTEx
rs880034	SAMD12	cis	Whole Blood	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:119609400-119633600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr8:119627600-119633600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr8:119632400-119633400	Enhancers	Left Ventricle	heart
4	chr8:119632600-119633400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
5	chr8:119632600-119634000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
6	chr8:119632600-119635200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr8:119632800-119633400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr8:119632800-119633400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr8:119632800-119633400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
10	chr8:119632800-119633400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr8:119632800-119633400	Bivalent/Poised TSS	Primary T cells from cord blood	blood
12	chr8:119632800-119633400	Flanking Active TSS	Brain Anterior Caudate	brain
13	chr8:119632800-119633400	Flanking Active TSS	Duodenum Mucosa	Duodenum
14	chr8:119632800-119633400	Enhancers	Fetal Lung	lung
15	chr8:119632800-119633400	Enhancers	Ovary	ovary
16	chr8:119632800-119633400	Enhancers	HUVEC	blood vessel
17	chr8:119632800-119633600	Flanking Active TSS	Brain Angular Gyrus	brain
18	chr8:119632800-119633600	Flanking Active TSS	Brain Cingulate Gyrus	brain
19	chr8:119632800-119633600	Flanking Active TSS	Brain Hippocampus Middle	brain
20	chr8:119632800-119633600	Enhancers	Spleen	Spleen
21	chr8:119632800-119633800	Flanking Active TSS	NHEK	skin
22	chr8:119632800-119634000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr8:119632800-119634200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr8:119632800-119635000	Active TSS	Colonic Mucosa	Colon
25	chr8:119632800-119635000	Active TSS	Rectal Smooth Muscle	rectum
26	chr8:119633000-119633400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr8:119633000-119633400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
28	chr8:119633000-119633400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
29	chr8:119633000-119633400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
30	chr8:119633000-119633400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
31	chr8:119633000-119633400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
32	chr8:119633000-119633400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
33	chr8:119633000-119633400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
34	chr8:119633000-119633400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
35	chr8:119633000-119633400	Enhancers	Right Ventricle	heart
36	chr8:119633000-119633400	Bivalent Enhancer	HepG2	liver
37	chr8:119633000-119633600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr8:119633000-119633600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
39	chr8:119633000-119633600	Bivalent Enhancer	Fetal Muscle Leg	muscle
40	chr8:119633000-119633800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
41	chr8:119633000-119633800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr8:119633000-119634000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
43	chr8:119633000-119634000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
44	chr8:119633000-119634000	Flanking Active TSS	Primary B cells from peripheral blood	blood
45	chr8:119633000-119634000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
46	chr8:119633000-119634000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr8:119633000-119634200	Flanking Active TSS	Liver	Liver
48	chr8:119633000-119634600	Active TSS	Esophagus	oesophagus
49	chr8:119633000-119634600	Active TSS	Right Atrium	heart
50	chr8:119633000-119634800	Active TSS	H9 Cell Line	embryonic stem cell

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