Variant report

Variant	rs3797310
Chromosome Location	chr5:42756940-42756941
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GHR-4	chr5:42756928-42756987	NONHSAT101224

Extended variants
information (count: 114 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs1035516	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1046068	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10462041	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10941585	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10941586	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10941587	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10941592	0.85[EUR][1000 genomes]
rs10941593	0.85[EUR][1000 genomes]
rs11952526	0.87[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11953691	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11957181	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12054838	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12055087	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12055266	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12187466	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12187996	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12516157	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12516954	0.81[EUR][1000 genomes]
rs12517112	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12518414	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12519443	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12519532	0.85[EUR][1000 genomes]
rs12521615	0.85[EUR][1000 genomes]
rs12522458	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13178745	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1345825	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1364024	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1364026	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1364027	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1423654	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1593070	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17231271	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1862628	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2113086	0.88[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2161600	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28919269	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28919892	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28919916	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2910871	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2973028	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3797311	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3866438	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3870358	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3870359	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3906418	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4143864	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4242120	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4242121	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4866794	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4866797	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4866798	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4866799	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4866802	0.85[EUR][1000 genomes]
rs4866949	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4866952	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4866954	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4866958	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4866959	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4866961	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4866962	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4866963	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4866966	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4866967	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55651065	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55660133	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55687632	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55688895	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55801363	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55881749	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55928305	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56273800	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56300261	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56394865	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56848171	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58429632	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59184964	0.81[EUR][1000 genomes]
rs60008560	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62370873	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62370874	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62370911	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62370912	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62370950	0.84[EUR][1000 genomes]
rs62370951	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62370952	0.83[EUR][1000 genomes]
rs62370953	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62370955	0.83[EUR][1000 genomes]
rs62372042	0.85[EUR][1000 genomes]
rs62373001	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62373002	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6865453	0.88[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6899268	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs722677	0.97[ASN][1000 genomes]
rs722678	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7579	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7708223	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7708337	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7725776	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7725961	0.88[CHB][hapmap];0.91[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7730190	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7734918	0.88[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8180394	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8180482	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9637794	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
2	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases
3	nsv1031160	chr5:42610090-42843255	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1019696	chr5:42610090-42844191	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv597886	chr5:42610409-42854408	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1029933	chr5:42611976-42833385	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv537735	chr5:42611976-42833385	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
9	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
10	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
11	nsv523033	chr5:42752037-42919685	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3797310	CCDC152	cis	Artery Tibial	GTEx
rs3797310	SEPP1	Cis_1M	lymphoblastoid	RTeQTL
rs3797310	CCDC152	cis	Artery Aorta	GTEx

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42756600-42757200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr5:42756600-42757400	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr5:42756600-42757400	Active TSS	K562	blood
4	chr5:42756600-42757800	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr5:42756600-42757800	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr5:42756600-42757800	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr5:42756600-42757800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr5:42756600-42758000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr5:42756600-42758000	Active TSS	Fetal Brain Female	brain
10	chr5:42756800-42757000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr5:42756800-42757000	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr5:42756800-42757000	Flanking Active TSS	Primary hematopoietic stem cells	blood
13	chr5:42756800-42757000	Active TSS	Brain Germinal Matrix	brain
14	chr5:42756800-42757000	Active TSS	Fetal Lung	lung
15	chr5:42756800-42757000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
16	chr5:42756800-42757200	Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr5:42756800-42757200	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr5:42756800-42757200	Active TSS	Primary B cells from peripheral blood	blood
19	chr5:42756800-42757200	Bivalent/Poised TSS	Primary T cells fromperipheralblood	blood
20	chr5:42756800-42757200	Active TSS	Primary T helper cells fromperipheralblood	blood
21	chr5:42756800-42757200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
22	chr5:42756800-42757200	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
23	chr5:42756800-42757200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr5:42756800-42757200	Bivalent/Poised TSS	Cortex derived primary cultured neurospheres	brain
25	chr5:42756800-42757200	Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr5:42756800-42757200	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
27	chr5:42756800-42757200	Active TSS	Fetal Muscle Leg	muscle
28	chr5:42756800-42757200	Active TSS	Gastric	stomach
29	chr5:42756800-42757200	Enhancers	Left Ventricle	heart
30	chr5:42756800-42757200	Active TSS	Ovary	ovary
31	chr5:42756800-42757200	Active TSS	Right Ventricle	heart
32	chr5:42756800-42757200	Active TSS	Stomach Smooth Muscle	stomach
33	chr5:42756800-42757200	Active TSS	HUVEC	blood vessel
34	chr5:42756800-42757400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr5:42756800-42757400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr5:42756800-42757400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
37	chr5:42756800-42757400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
38	chr5:42756800-42757400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
39	chr5:42756800-42757400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr5:42756800-42757400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr5:42756800-42757400	Active TSS	Adipose Nuclei	Adipose
42	chr5:42756800-42757400	Active TSS	Brain Cingulate Gyrus	brain
43	chr5:42756800-42757400	Active TSS	Fetal Thymus	thymus
44	chr5:42756800-42757400	Active TSS	Pancreas	Pancrea
45	chr5:42756800-42757400	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
46	chr5:42756800-42757400	Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr5:42756800-42757400	Active TSS	HMEC	breast
48	chr5:42756800-42757400	Active TSS	HSMM	muscle
49	chr5:42756800-42757400	Active TSS	NHDF-Ad	bronchial
50	chr5:42756800-42757400	Active TSS	Osteobl	bone

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