Variant report

Variant	rs6603943
Chromosome Location	chr1:77861754-77861755
allele	A/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	GATA3	chr1:77861220-77861865	SK-N-SH	brain:	n/a	chr1:77861549-77861556 chr1:77861542-77861563 chr1:77861549-77861556 chr1:77861545-77861561 chr1:77861565-77861574 chr1:77861549-77861556
2	MAFK	chr1:77861712-77861991	IMR90	lung:	n/a	chr1:77861859-77861875 chr1:77861859-77861874 chr1:77861854-77861874
3	POLR2A	chr1:77861511-77861924	K562	blood:	n/a	n/a
4	MAFF	chr1:77861729-77861999	HepG2	liver:	n/a	chr1:77861858-77861876
5	MAFK	chr1:77861690-77862018	HepG2	liver:	n/a	chr1:77861859-77861875 chr1:77861859-77861874 chr1:77861854-77861874
6	MAFK	chr1:77861728-77862000	HepG2	liver:	n/a	chr1:77861859-77861875 chr1:77861859-77861874 chr1:77861854-77861874

Variant related genes	Relation type
ENSG00000221664	TF binding region

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10873935	0.85[ASN][1000 genomes]
rs11162329	0.85[ASN][1000 genomes]
rs11162335	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12043793	0.85[ASN][1000 genomes]
rs17100509	0.97[ASN][1000 genomes]
rs17100513	0.97[ASN][1000 genomes]
rs4949800	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6673059	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7546116	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005183	chr1:77728990-77949309	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv535010	chr1:77728990-77949309	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv932557	chr1:77730247-77958687	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1003714	chr1:77756861-77949309	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv470719	chr1:77774413-78269207	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	nsv546591	chr1:77774413-78269207	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77845200-77878000	Weak transcription	Primary T cells from cord blood	blood
2	chr1:77845200-77878400	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr1:77854000-77865200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr1:77854200-77863600	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr1:77854200-77864200	Weak transcription	Brain Germinal Matrix	brain
6	chr1:77854800-77862600	Weak transcription	Aorta	Aorta
7	chr1:77855000-77863800	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr1:77859200-77862600	Enhancers	NHDF-Ad	bronchial
9	chr1:77859400-77865600	Enhancers	Brain Anterior Caudate	brain
10	chr1:77859800-77865600	Enhancers	Brain Cingulate Gyrus	brain
11	chr1:77859800-77866200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:77860000-77862800	Enhancers	Osteobl	bone
13	chr1:77860000-77866200	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr1:77860000-77866600	Enhancers	Brain Hippocampus Middle	brain
15	chr1:77860200-77862800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:77860400-77864000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:77860800-77862800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:77860800-77866000	Enhancers	Brain Angular Gyrus	brain
19	chr1:77861000-77866400	Enhancers	Brain Substantia Nigra	brain
20	chr1:77861200-77861800	Genic enhancers	HSMM	muscle
21	chr1:77861200-77862400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:77861200-77865000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:77861200-77865000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:77861400-77862200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:77861400-77862400	Weak transcription	HSMMtube	muscle
26	chr1:77861400-77863200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr1:77861400-77863600	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr1:77861400-77863800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr1:77861400-77865200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:77861400-77865200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:77861400-77865600	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr1:77861600-77862000	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr1:77861600-77864000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr1:77861600-77865600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:77861600-77871800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links