Variant report

Variant	rs6680479
Chromosome Location	chr1:9932900-9932901
allele	G/T
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	FOSL2	chr1:9932661-9933234	SK-N-SH	brain:	n/a	chr1:9933099-9933113 chr1:9932959-9932971 chr1:9932961-9932969
2	FOS	chr1:9932834-9933002	MCF10A-Er-Src	breast:	n/a	chr1:9932959-9932971 chr1:9932961-9932969
3	FOS	chr1:9932858-9933025	MCF10A-Er-Src	breast:	n/a	chr1:9932959-9932971 chr1:9932961-9932969
4	MAZ	chr1:9932473-9933253	IMR90	lung:	n/a	chr1:9932492-9932502 chr1:9932960-9932969 chr1:9932884-9932894 chr1:9932488-9932507 chr1:9932492-9932502 chr1:9932491-9932504 chr1:9932493-9932502 chr1:9932492-9932503
5	POLR2A	chr1:9932891-9932992	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:9932776..9936853-chr1:9938064..9942727,5	K562	blood:
2	chr1:9931884..9936639-chr1:9967934..9971147,6	MCF-7	breast:

Variant related genes	Relation type
CTNNBIP1	TF binding region
ENSG00000178585	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2379109	1.00[AMR][1000 genomes]
rs6696382	1.00[AMR][1000 genomes]
rs74054134	1.00[AMR][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	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
2	nsv871610	chr1:9655795-10008221	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv3372906	chr1:9838995-10052992	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv871146	chr1:9897001-9951288	Genic enhancers Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv545380	chr1:9918183-9987007	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv1012469	chr1:9925714-10147796	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS 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 miRNA target site	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9904600-9935000	Weak transcription	Osteobl	bone
2	chr1:9904800-9946000	Weak transcription	Fetal Kidney	kidney
3	chr1:9910000-9935000	Weak transcription	NHLF	lung
4	chr1:9915800-9935200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:9917800-9934400	Strong transcription	Fetal Intestine Small	intestine
6	chr1:9918600-9943800	Weak transcription	Small Intestine	intestine
7	chr1:9920200-9935200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr1:9921000-9934800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:9921800-9934800	Weak transcription	Right Atrium	heart
10	chr1:9922000-9933200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr1:9923800-9935200	Weak transcription	A549	lung
12	chr1:9924200-9934400	Strong transcription	Fetal Stomach	stomach
13	chr1:9924200-9935200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:9924200-9935200	Weak transcription	Brain Substantia Nigra	brain
15	chr1:9925800-9933400	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr1:9925800-9933600	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr1:9926200-9933200	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr1:9927400-9933200	Strong transcription	Adipose Nuclei	Adipose
19	chr1:9927600-9941800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr1:9927800-9933000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:9928000-9933000	Strong transcription	Brain Cingulate Gyrus	brain
22	chr1:9928000-9934800	Weak transcription	Dnd41	blood
23	chr1:9928000-9935000	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr1:9928000-9935000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr1:9928000-9935200	Weak transcription	GM12878-XiMat	blood
26	chr1:9928400-9935200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:9928400-9938000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:9929000-9933200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr1:9929400-9933400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr1:9930200-9941800	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr1:9930400-9933800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr1:9930400-9934800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr1:9930400-9935200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr1:9930600-9935000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr1:9930800-9933200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr1:9930800-9934000	Genic enhancers	Fetal Muscle Leg	muscle
37	chr1:9930800-9934600	Weak transcription	Brain Angular Gyrus	brain
38	chr1:9930800-9942200	Weak transcription	Primary hematopoietic stem cells	blood
39	chr1:9930800-9949600	Weak transcription	Fetal Lung	lung
40	chr1:9931000-9933400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:9931000-9934800	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr1:9931000-9934800	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr1:9931000-9934800	Weak transcription	Liver	Liver
44	chr1:9931000-9935000	Weak transcription	Primary B cells from cord blood	blood
45	chr1:9931000-9935000	Genic enhancers	Fetal Muscle Trunk	muscle
46	chr1:9931000-9935200	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr1:9931000-9935200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr1:9931200-9935200	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr1:9931400-9933400	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr1:9931400-9934800	Weak transcription	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links