Variant report

Variant	rs6668894
Chromosome Location	chr1:151047641-151047642
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:151042783..151045327-chr1:151046112..151049113,3	K562	blood:

Variant related genes	Relation type
ENSG00000143458	Chromatin interaction
ENSG00000197622	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10788798	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10788799	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11204777	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11204778	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11204780	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12039334	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12039542	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12040729	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs12117163	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1524773	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1969442	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2140709	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2902810	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3738481	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3806386	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3806387	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4970939	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4970993	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4970998	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4970999	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4971002	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4971003	0.84[EUR][1000 genomes]
rs4971005	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4971006	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4971007	0.84[EUR][1000 genomes]
rs4971008	0.80[EUR][1000 genomes]
rs5023311	0.80[EUR][1000 genomes]
rs6587553	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6657593	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6694158	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7366148	0.86[AMR][1000 genomes];0.88[EUR][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	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6668894	LYSMD1	Cis_1M	lymphoblastoid	RTeQTL
rs6668894	BNIPL	cis	Thyroid	GTEx
rs6668894	CDC42SE1	Cis_1M	lymphoblastoid	RTeQTL
rs6668894	BNIPL	cis	lung	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151043600-151048200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:151043600-151048800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:151043600-151049600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:151043600-151050200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:151043800-151056200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:151044000-151048800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr1:151044000-151062800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:151044000-151066800	Weak transcription	Ovary	ovary
9	chr1:151044000-151079600	Weak transcription	Spleen	Spleen
10	chr1:151044000-151080600	Weak transcription	Esophagus	oesophagus
11	chr1:151044200-151049200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:151044200-151069800	Weak transcription	HSMM	muscle
13	chr1:151044200-151070800	Weak transcription	Fetal Lung	lung
14	chr1:151044200-151080200	Weak transcription	Aorta	Aorta
15	chr1:151044400-151048400	Weak transcription	HUVEC	blood vessel
16	chr1:151044400-151061600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr1:151044400-151062200	Weak transcription	Liver	Liver
18	chr1:151044400-151079000	Weak transcription	Left Ventricle	heart
19	chr1:151044400-151079600	Weak transcription	Lung	lung
20	chr1:151044400-151090200	Weak transcription	Gastric	stomach
21	chr1:151044400-151090400	Weak transcription	Right Ventricle	heart
22	chr1:151044400-151103600	Weak transcription	Small Intestine	intestine
23	chr1:151044600-151048400	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr1:151044600-151049800	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr1:151044600-151052000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr1:151044600-151052000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:151044600-151054200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr1:151044600-151061200	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr1:151044600-151069600	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr1:151044600-151069800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:151044600-151069800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:151044600-151070000	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr1:151044600-151076000	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr1:151044600-151080400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr1:151044600-151080600	Weak transcription	Brain Anterior Caudate	brain
36	chr1:151044600-151081000	Weak transcription	Colon Smooth Muscle	Colon
37	chr1:151044800-151048400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr1:151044800-151061400	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr1:151044800-151062800	Weak transcription	Brain Hippocampus Middle	brain
40	chr1:151044800-151065400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr1:151044800-151066200	Weak transcription	Brain Substantia Nigra	brain
42	chr1:151044800-151069800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:151044800-151070400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr1:151044800-151079600	Weak transcription	Primary B cells from peripheral blood	blood
45	chr1:151044800-151080200	Weak transcription	Fetal Brain Female	brain
46	chr1:151044800-151089400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:151044800-151098800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr1:151045000-151048000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr1:151045000-151048200	Weak transcription	Pancreas	Pancrea
50	chr1:151045000-151048400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links