Variant report

Variant	rs4971006
Chromosome Location	chr1:151105824-151105825
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr1:151105411-151106236	H1-hESC	embryonic stem cell:	n/a	n/a
2	E2F6	chr1:151103259-151106011	H1-hESC	embryonic stem cell:	n/a	chr1:151103613-151103620 chr1:151103613-151103620 chr1:151103612-151103621 chr1:151103612-151103624 chr1:151103969-151103979 chr1:151103613-151103620
3	POLR2A	chr1:151105788-151106035	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAX	chr1:151105069-151106289	H1-hESC	embryonic stem cell:	n/a	n/a
5	SIN3A	chr1:151105540-151106276	H1-hESC	embryonic stem cell:	n/a	n/a
6	ZNF143	chr1:151105660-151105950	H1-hESC	embryonic stem cell:	n/a	n/a
7	TBP	chr1:151105816-151106071	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:151103786..151106331-chr1:151117499..151120768,3	MCF-7	breast:
2	chr1:151104790..151107252-chr1:151107376..151109485,2	K562	blood:
3	chr1:151104617..151106812-chr1:151117447..151119044,2	MCF-7	breast:
4	chr1:151104720..151106721-chr1:151225505..151227550,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261168	TF binding region
SEMA6C	TF binding region
ENSG00000159352	Chromatin interaction
ENSG00000143434	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10788798	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10788799	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10788800	0.81[ASN][1000 genomes]
rs11204777	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11204778	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11204780	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12117163	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1524773	0.84[ASN][1000 genomes]
rs2140709	0.84[ASN][1000 genomes]
rs3738481	0.84[ASN][1000 genomes]
rs4357530	0.81[ASN][1000 genomes]
rs4970993	0.84[ASN][1000 genomes]
rs4970998	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4970999	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4971002	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4971003	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4971005	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4971007	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4971008	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs5023311	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61819219	0.81[ASN][1000 genomes]
rs6656450	0.81[ASN][1000 genomes]
rs6668894	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6676190	0.81[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	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
5	nsv872422	chr1:151098077-151115186	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv872423	chr1:151100612-151115997	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	esv3399787	chr1:151104353-151106901	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4971006	BNIPL	cis	lung	GTEx
rs4971006	BNIPL	cis	Thyroid	GTEx
rs4971006	LYSMD1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151079800-151106200	Weak transcription	HSMMtube	muscle
2	chr1:151079800-151114800	Weak transcription	HSMM	muscle
3	chr1:151097800-151106000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:151103200-151106000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr1:151103400-151106000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
6	chr1:151103400-151106200	Active TSS	H9 Cell Line	embryonic stem cell
7	chr1:151103400-151106400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
8	chr1:151103600-151106200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
9	chr1:151103600-151106200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
10	chr1:151104000-151106000	Enhancers	Pancreas	Pancrea
11	chr1:151104000-151114800	Weak transcription	Psoas Muscle	Psoas
12	chr1:151104200-151106000	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:151104200-151106200	Enhancers	Fetal Brain Male	brain
14	chr1:151104200-151107800	Weak transcription	Liver	Liver
15	chr1:151104400-151106000	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr1:151104400-151106200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
17	chr1:151104400-151106600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr1:151104400-151106800	Weak transcription	Brain Angular Gyrus	brain
19	chr1:151104400-151107600	Weak transcription	GM12878-XiMat	blood
20	chr1:151104400-151110400	Weak transcription	NHLF	lung
21	chr1:151104400-151111200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:151104400-151116600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr1:151104400-151117000	Weak transcription	Fetal Kidney	kidney
24	chr1:151104400-151118000	Weak transcription	Aorta	Aorta
25	chr1:151104600-151106000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:151104600-151106200	Weak transcription	Brain Hippocampus Middle	brain
27	chr1:151104600-151106200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr1:151104600-151106200	Weak transcription	Fetal Lung	lung
29	chr1:151104600-151106600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:151104600-151106600	Weak transcription	Brain Anterior Caudate	brain
31	chr1:151104600-151106600	Weak transcription	HUVEC	blood vessel
32	chr1:151104600-151107600	Weak transcription	Brain Substantia Nigra	brain
33	chr1:151104600-151108200	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr1:151104600-151109000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr1:151104600-151117400	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr1:151104600-151118200	Weak transcription	Primary T cells from cord blood	blood
37	chr1:151104800-151106000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
38	chr1:151104800-151106000	Strong transcription	Skeletal Muscle Male	skeletal muscle
39	chr1:151104800-151106200	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr1:151104800-151106600	Bivalent Enhancer	Brain Germinal Matrix	brain
41	chr1:151104800-151106800	Weak transcription	Duodenum Mucosa	Duodenum
42	chr1:151104800-151107600	Weak transcription	Lung	lung
43	chr1:151104800-151108200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:151104800-151108400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr1:151104800-151115600	Weak transcription	Primary hematopoietic stem cells	blood
46	chr1:151105000-151106000	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr1:151105000-151106000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
48	chr1:151105000-151106200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr1:151105000-151114800	Strong transcription	Fetal Brain Female	brain
50	chr1:151105000-151114800	Weak transcription	Right Atrium	heart

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