Variant report

Variant	rs12093618
Chromosome Location	chr1:47074141-47074142
allele	A/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	POLR2A	chr1:47073187-47074368	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:47073470-47074299	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:47069986..47078443-chr1:47078833..47084050,15	K562	blood:
2	chr1:47073700..47076420-chr1:47091166..47093080,2	K562	blood:
3	chr1:47061375..47064454-chr1:47072882..47074737,3	K562	blood:
4	chr1:47068458..47072661-chr1:47073535..47079342,7	MCF-7	breast:

Variant related genes	Relation type
MKNK1	TF binding region
ENSG00000142961	Chromatin interaction
ENSG00000079277	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11211305	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs11211307	1.00[YRI][hapmap]
rs11211308	0.83[AFR][1000 genomes]
rs11211310	0.83[AFR][1000 genomes]
rs11211311	1.00[YRI][hapmap]
rs11211313	0.83[AFR][1000 genomes]
rs11211315	0.83[AFR][1000 genomes]
rs11211316	0.83[AFR][1000 genomes]
rs11211318	0.88[AFR][1000 genomes]
rs11211321	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11211322	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12080601	0.83[AFR][1000 genomes]
rs12083666	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12088719	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs12090191	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12092171	0.80[AFR][1000 genomes]
rs12096548	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs17102443	1.00[MEX][hapmap]
rs3766235	0.83[AFR][1000 genomes]
rs41305866	0.83[AFR][1000 genomes]
rs56089465	0.83[AFR][1000 genomes]
rs61783117	0.83[AFR][1000 genomes]
rs61783120	0.83[AFR][1000 genomes]
rs61783122	0.83[AFR][1000 genomes]
rs61783123	0.85[AFR][1000 genomes]
rs6681420	0.83[AMR][1000 genomes]
rs682000	1.00[MEX][hapmap]

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	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1009193	chr1:46939999-47085667	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv870392	chr1:47040676-47095097	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47070000-47077600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:47070000-47078800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:47070400-47081200	Weak transcription	Fetal Brain Male	brain
4	chr1:47070600-47074600	Weak transcription	HSMM	muscle
5	chr1:47070600-47077200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:47070600-47077400	Weak transcription	NH-A	brain
7	chr1:47070600-47077600	Weak transcription	Fetal Heart	heart
8	chr1:47070600-47078400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr1:47070800-47074200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr1:47070800-47074400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr1:47070800-47074600	Weak transcription	Stomach Mucosa	stomach
12	chr1:47070800-47076600	Weak transcription	Hela-S3	cervix
13	chr1:47070800-47077200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr1:47070800-47077400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr1:47070800-47077400	Weak transcription	A549	lung
16	chr1:47071000-47075600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:47071000-47078400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr1:47071200-47077200	Weak transcription	K562	blood
19	chr1:47071600-47077200	Strong transcription	Fetal Stomach	stomach
20	chr1:47071800-47074600	Genic enhancers	Fetal Muscle Leg	muscle
21	chr1:47071800-47079200	Weak transcription	Dnd41	blood
22	chr1:47072000-47074200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:47072000-47077000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr1:47072000-47077600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr1:47072000-47079000	Strong transcription	Fetal Intestine Small	intestine
26	chr1:47072200-47074200	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:47072200-47074600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr1:47072200-47074600	Weak transcription	Fetal Thymus	thymus
29	chr1:47072400-47077000	Strong transcription	Lung	lung
30	chr1:47072400-47077000	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr1:47073000-47074200	Genic enhancers	Adipose Nuclei	Adipose
32	chr1:47073000-47074200	Enhancers	Right Atrium	heart
33	chr1:47073000-47077400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr1:47073200-47075800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr1:47073200-47077000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr1:47073200-47077000	Strong transcription	GM12878-XiMat	blood
37	chr1:47073200-47077200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:47073400-47074200	Genic enhancers	Brain Hippocampus Middle	brain
39	chr1:47073400-47074200	Genic enhancers	Fetal Muscle Trunk	muscle
40	chr1:47073400-47074800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:47073400-47075200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
42	chr1:47073400-47076200	Strong transcription	Colonic Mucosa	Colon
43	chr1:47073400-47076600	Strong transcription	Placenta	Placenta
44	chr1:47073400-47076600	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr1:47073400-47077000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr1:47073400-47077200	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr1:47073400-47077200	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr1:47073400-47079000	Strong transcription	Fetal Intestine Large	intestine
49	chr1:47073600-47074200	Genic enhancers	Aorta	Aorta
50	chr1:47073600-47074200	Genic enhancers	Brain Anterior Caudate	brain

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