Variant report

Variant	rs56682893
Chromosome Location	chr1:10115442-10115443
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	RCOR1	chr1:10115387-10116918	IMR90	lung:	n/a	n/a
2	POLR2A	chr1:10115178-10115681	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:10108005..10110082-chr1:10115252..10117547,2	K562	blood:

Variant related genes	Relation type
PGAM1P11	TF binding region
ENSG00000224340	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11801988	1.00[EUR][1000 genomes]
rs11803995	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11804755	0.81[AFR][1000 genomes]
rs11808311	1.00[EUR][1000 genomes]
rs28671063	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41280788	1.00[EUR][1000 genomes]
rs56760324	1.00[EUR][1000 genomes]
rs57216908	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58453167	0.84[EUR][1000 genomes]
rs61134758	0.94[EUR][1000 genomes]
rs61462323	1.00[EUR][1000 genomes]
rs6676768	0.84[EUR][1000 genomes]
rs6693686	1.00[EUR][1000 genomes]
rs6701103	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72859590	1.00[EUR][1000 genomes]
rs72861431	1.00[EUR][1000 genomes]
rs72861447	1.00[EUR][1000 genomes]
rs72861453	1.00[EUR][1000 genomes]
rs9661116	1.00[EUR][1000 genomes]
rs9661131	0.84[AFR][1000 genomes];1.00[EUR][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	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
2	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
3	nsv1012301	chr1:9963962-10118393	Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv534853	chr1:9963962-10118393	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv1001742	chr1:9971776-10116767	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	nsv527217	chr1:10093457-10257167	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10094800-10119400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:10095000-10116000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr1:10095000-10116200	Weak transcription	HSMM	muscle
4	chr1:10095000-10127800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:10095000-10147600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr1:10095200-10134400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr1:10095400-10115600	Weak transcription	HUVEC	blood vessel
8	chr1:10098800-10116000	Weak transcription	Hela-S3	cervix
9	chr1:10098800-10131200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr1:10103000-10116200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:10106400-10134000	Weak transcription	Colonic Mucosa	Colon
12	chr1:10106800-10116600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:10106800-10118000	Weak transcription	Fetal Kidney	kidney
14	chr1:10106800-10128400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:10106800-10134200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:10106800-10155400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr1:10107000-10115600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:10107000-10115600	Weak transcription	Lung	lung
19	chr1:10107000-10117600	Weak transcription	Aorta	Aorta
20	chr1:10107000-10118600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr1:10107000-10125200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr1:10107000-10125200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr1:10107000-10125400	Weak transcription	Small Intestine	intestine
24	chr1:10107000-10140600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:10107200-10116600	Weak transcription	Right Atrium	heart
26	chr1:10107200-10116800	Weak transcription	Gastric	stomach
27	chr1:10107200-10118600	Weak transcription	Spleen	Spleen
28	chr1:10107200-10118800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr1:10107200-10124000	Weak transcription	Fetal Brain Female	brain
30	chr1:10107200-10125200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:10107200-10125200	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr1:10107400-10116000	Weak transcription	Rectal Smooth Muscle	rectum
33	chr1:10107400-10124000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr1:10107400-10124200	Strong transcription	Fetal Intestine Small	intestine
35	chr1:10107400-10125200	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr1:10107400-10125400	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr1:10107400-10135200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr1:10107400-10165400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr1:10107600-10116000	Weak transcription	Adipose Nuclei	Adipose
40	chr1:10107600-10118000	Weak transcription	Esophagus	oesophagus
41	chr1:10107600-10125400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr1:10108000-10115800	Strong transcription	Fetal Stomach	stomach
43	chr1:10109000-10115600	Weak transcription	Colon Smooth Muscle	Colon
44	chr1:10109000-10116800	Weak transcription	Pancreas	Pancrea
45	chr1:10109000-10126400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr1:10109400-10158400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr1:10111200-10118200	Weak transcription	Fetal Thymus	thymus
48	chr1:10111400-10118600	Weak transcription	Fetal Muscle Trunk	muscle
49	chr1:10111400-10125200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr1:10111400-10127000	Weak transcription	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links