Variant report

Variant	rs4970939
Chromosome Location	chr1:151045248-151045249
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:150977392..150983338-chr1:151040807..151046211,16	MCF-7	breast:
2	chr1:151043812..151045810-chr1:151065348..151067494,2	K562	blood:
3	chr1:150997053..150997598-chr1:151044515..151045335,3	MCF-7	breast:
4	chr1:151043637..151045310-chr1:151061634..151063146,2	MCF-7	breast:
5	chr1:151000849..151004136-chr1:151043439..151047441,3	K562	blood:
6	chr1:151044680..151046429-chr1:151136336..151137837,2	K562	blood:
7	chr1:150978947..150982308-chr1:151041500..151045951,4	K562	blood:
8	chr1:151043837..151046087-chr1:151112231..151114471,2	K562	blood:
9	chr1:151042151..151045476-chr1:151127754..151130933,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000143409	Chromatin interaction
ENSG00000163154	Chromatin interaction
ENSG00000143363	Chromatin interaction
ENSG00000163156	Chromatin interaction
ENSG00000143458	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10788798	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10788799	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11204777	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11204778	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11204780	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12039334	0.88[EUR][1000 genomes]
rs12039542	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12117163	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1524773	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs15740	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1969442	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2140709	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2902810	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3738481	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3806386	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3806387	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4970936	0.84[AMR][1000 genomes]
rs4970940	0.80[AMR][1000 genomes]
rs4970993	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4970998	0.87[EUR][1000 genomes]
rs4970999	0.83[EUR][1000 genomes]
rs4971003	0.82[EUR][1000 genomes]
rs4971005	0.82[EUR][1000 genomes]
rs4971007	0.82[EUR][1000 genomes]
rs6587553	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6657593	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6668894	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6694158	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7366148	0.82[AMR][1000 genomes];0.89[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
rs4970939	BNIPL	cis	Thyroid	GTEx
rs4970939	BNIPL	cis	lung	GTEx
rs4970939	LYSMD1	Cis_1M	lymphoblastoid	RTeQTL
rs4970939	CDC42SE1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

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	chr1:151043800-151047200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:151043800-151056200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:151044000-151046400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr1:151044000-151046400	Weak transcription	NH-A	brain
9	chr1:151044000-151047000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr1:151044000-151047400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr1:151044000-151048800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr1:151044000-151062800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr1:151044000-151066800	Weak transcription	Ovary	ovary
14	chr1:151044000-151079600	Weak transcription	Spleen	Spleen
15	chr1:151044000-151080600	Weak transcription	Esophagus	oesophagus
16	chr1:151044200-151045600	Enhancers	HepG2	liver
17	chr1:151044200-151046000	Enhancers	Primary T cells fromperipheralblood	blood
18	chr1:151044200-151047600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:151044200-151049200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:151044200-151069800	Weak transcription	HSMM	muscle
21	chr1:151044200-151070800	Weak transcription	Fetal Lung	lung
22	chr1:151044200-151080200	Weak transcription	Aorta	Aorta
23	chr1:151044400-151045600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:151044400-151045600	Weak transcription	Fetal Muscle Leg	muscle
25	chr1:151044400-151045600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr1:151044400-151046600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr1:151044400-151047000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr1:151044400-151047000	Weak transcription	HMEC	breast
29	chr1:151044400-151047200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr1:151044400-151048400	Weak transcription	HUVEC	blood vessel
31	chr1:151044400-151061600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr1:151044400-151062200	Weak transcription	Liver	Liver
33	chr1:151044400-151079000	Weak transcription	Left Ventricle	heart
34	chr1:151044400-151079600	Weak transcription	Lung	lung
35	chr1:151044400-151090200	Weak transcription	Gastric	stomach
36	chr1:151044400-151090400	Weak transcription	Right Ventricle	heart
37	chr1:151044400-151103600	Weak transcription	Small Intestine	intestine
38	chr1:151044600-151045400	Weak transcription	Fetal Intestine Small	intestine
39	chr1:151044600-151045400	Weak transcription	Fetal Stomach	stomach
40	chr1:151044600-151045600	Weak transcription	Primary T cells from cord blood	blood
41	chr1:151044600-151045800	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr1:151044600-151045800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr1:151044600-151045800	Weak transcription	Stomach Smooth Muscle	stomach
44	chr1:151044600-151046400	Weak transcription	Fetal Intestine Large	intestine
45	chr1:151044600-151046800	Weak transcription	Thymus	Thymus
46	chr1:151044600-151047000	Weak transcription	Rectal Smooth Muscle	rectum
47	chr1:151044600-151047000	Weak transcription	NHDF-Ad	bronchial
48	chr1:151044600-151047200	Weak transcription	Fetal Brain Male	brain
49	chr1:151044600-151047600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr1:151044600-151048400	Weak transcription	Primary monocytes fromperipheralblood	blood

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