Variant report

Variant	rs1419089
Chromosome Location	chr6:78078636-78078637
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HTR1B-1	chr6:78078603-78078829	XLOC_005769

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10455106	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10455329	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10755354	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10943436	0.86[ASN][1000 genomes]
rs10943437	0.89[ASN][1000 genomes]
rs10943439	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10943451	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1115314	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11750960	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11755232	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12192404	0.92[ASN][1000 genomes]
rs12525774	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1342624	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1342627	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1342629	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1342633	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1342634	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1342635	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1342638	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1361759	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1418584	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1418585	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1418586	0.92[ASN][1000 genomes]
rs1539580	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1557160	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1592219	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16879515	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1857201	0.88[ASN][1000 genomes]
rs1935724	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1935729	0.91[ASN][1000 genomes]
rs1935732	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1935737	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2153886	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2153891	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2211408	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2211411	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2226150	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2226152	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2320293	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2874222	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2874223	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2874225	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4142468	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4142469	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4499894	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4708326	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4708327	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4708331	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6902991	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6904292	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6911609	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs756232	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7744314	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7752306	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7756606	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9341654	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9341655	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9341656	0.92[ASN][1000 genomes]
rs9341657	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9341659	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9341664	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9343587	0.92[ASN][1000 genomes]
rs9343588	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9343589	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9343590	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9343591	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9343592	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9343594	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9343604	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9350703	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9350706	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9352460	0.88[ASN][1000 genomes]
rs9352462	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9352463	0.88[ASN][1000 genomes]
rs9352477	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9359257	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9359258	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9359259	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9361214	0.86[ASN][1000 genomes]
rs9361215	0.86[ASN][1000 genomes]
rs9361216	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9361220	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9361223	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9361224	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017082	chr6:77585310-78258237	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv534282	chr6:77764575-78351994	Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1034979	chr6:77781244-78426249	Active TSS Weak transcription ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv538324	chr6:77781244-78426249	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1015307	chr6:77902559-78352291	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1028259	chr6:78059491-78709871	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv538325	chr6:78059491-78709871	Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:78076000-78079000	Active TSS	HUVEC	blood vessel
2	chr6:78076600-78079000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr6:78076600-78079000	Active TSS	NHEK	skin
4	chr6:78076600-78079200	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr6:78076800-78078800	Active TSS	Aorta	Aorta
6	chr6:78077000-78079000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr6:78077000-78079000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:78077000-78079000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr6:78077000-78079200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr6:78077200-78078800	Active TSS	Fetal Heart	heart
11	chr6:78077200-78079000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr6:78077200-78079400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:78077400-78079000	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr6:78077400-78079000	Active TSS	NHDF-Ad	bronchial
15	chr6:78077400-78079000	Active TSS	NHLF	lung
16	chr6:78077600-78079000	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr6:78077600-78079200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr6:78077600-78079200	Active TSS	Right Atrium	heart
19	chr6:78077800-78079000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr6:78077800-78079000	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr6:78077800-78079000	Active TSS	Adipose Nuclei	Adipose
22	chr6:78077800-78079000	Active TSS	Duodenum Mucosa	Duodenum
23	chr6:78077800-78079200	Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr6:78078000-78079000	Active TSS	H1 Cell Line	embryonic stem cell
25	chr6:78078000-78079000	Active TSS	HUES64 Cell Line	embryonic stem cell
26	chr6:78078000-78079000	Active TSS	iPS-15b Cell Line	embryonic stem cell
27	chr6:78078000-78079000	Active TSS	Rectal Mucosa Donor 31	rectum
28	chr6:78078000-78079000	Active TSS	NH-A	brain
29	chr6:78078000-78079200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr6:78078000-78079200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr6:78078000-78079200	Active TSS	Osteobl	bone
32	chr6:78078200-78078800	Active TSS	Brain Substantia Nigra	brain
33	chr6:78078200-78078800	Active TSS	Stomach Smooth Muscle	stomach
34	chr6:78078200-78079000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr6:78078200-78079000	Active TSS	H9 Cell Line	embryonic stem cell
36	chr6:78078200-78079000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr6:78078200-78079000	Active TSS	iPS-18 Cell Line	embryonic stem cell
38	chr6:78078200-78079000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr6:78078200-78079000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
40	chr6:78078200-78079000	Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr6:78078200-78079000	Active TSS	Primary B cells from cord blood	blood
42	chr6:78078200-78079000	Active TSS	Primary hematopoietic stem cells	blood
43	chr6:78078200-78079000	Active TSS	Primary hematopoietic stem cells short term culture	blood
44	chr6:78078200-78079000	Active TSS	Muscle Satellite Cultured Cells	--
45	chr6:78078200-78079000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr6:78078200-78079000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr6:78078200-78079000	Active TSS	Fetal Intestine Large	intestine
48	chr6:78078200-78079000	Active TSS	Fetal Lung	lung
49	chr6:78078200-78079000	Active TSS	Left Ventricle	heart
50	chr6:78078200-78079000	Active TSS	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links