Variant report

Variant	rs72825689
Chromosome Location	chr2:112790104-112790105
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:112786053..112788875-chr2:112788955..112792026,3	K562	blood:
2	chr2:112654547..112656932-chr2:112789072..112792767,3	MCF-7	breast:
3	chr2:112782602..112784298-chr2:112789398..112791163,2	K562	blood:

Variant related genes	Relation type
ENSG00000153208	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1546636	0.80[AMR][1000 genomes]
rs55730179	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55814634	0.80[AMR][1000 genomes]
rs55971930	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56097910	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56268477	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs56348540	0.80[AMR][1000 genomes]
rs56372767	0.80[AMR][1000 genomes]
rs72823496	0.80[AMR][1000 genomes]
rs72823502	0.80[AMR][1000 genomes]
rs72825604	0.80[AMR][1000 genomes]
rs72825612	0.80[AMR][1000 genomes]
rs72825617	0.80[AMR][1000 genomes]
rs72825620	0.80[AMR][1000 genomes]
rs72825639	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72825650	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72825667	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72825668	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72825671	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72825672	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72825673	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874863	chr2:112591224-113157344	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer 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	57 gene(s)	inside rSNPs	diseases
2	nsv874864	chr2:112617280-113104142	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv874865	chr2:112623098-113049274	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	nsv1013218	chr2:112645633-112908416	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv3333591	chr2:112669320-112892618	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv1002027	chr2:112679182-112861534	Weak transcription Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv1014787	chr2:112679182-112908416	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv535893	chr2:112679182-112908416	Strong transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv999746	chr2:112691270-112796083	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv1003129	chr2:112691270-112816694	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	esv2760607	chr2:112691282-112803423	Weak transcription Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv431491	chr2:112699350-112793981	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv515698	chr2:112699350-112795908	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv933392	chr2:112747230-112792349	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
15	esv1793068	chr2:112784234-112816694	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:112713200-112790600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr2:112769600-112791200	Weak transcription	Colonic Mucosa	Colon
3	chr2:112774400-112790200	Weak transcription	Right Atrium	heart
4	chr2:112781600-112790600	Weak transcription	Lung	lung
5	chr2:112783000-112790600	Weak transcription	Pancreas	Pancrea
6	chr2:112783200-112790600	Weak transcription	Esophagus	oesophagus
7	chr2:112783200-112802200	Weak transcription	Aorta	Aorta
8	chr2:112786200-112790600	Weak transcription	Left Ventricle	heart
9	chr2:112786200-112790600	Weak transcription	Stomach Mucosa	stomach
10	chr2:112786200-112798800	Weak transcription	K562	blood
11	chr2:112786400-112790600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr2:112786400-112796000	Weak transcription	Gastric	stomach
13	chr2:112788200-112790200	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr2:112789000-112790200	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr2:112789000-112790200	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr2:112789000-112790200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr2:112789000-112790800	Enhancers	Fetal Intestine Small	intestine
18	chr2:112789000-112790800	Enhancers	Small Intestine	intestine
19	chr2:112789000-112791000	Enhancers	Primary hematopoietic stem cells	blood
20	chr2:112789000-112791400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr2:112789000-112791400	Enhancers	Fetal Intestine Large	intestine
22	chr2:112789000-112791600	Enhancers	Placenta Amnion	Placenta Amnion
23	chr2:112789000-112792000	Enhancers	Duodenum Mucosa	Duodenum
24	chr2:112789000-112792000	Enhancers	HUVEC	blood vessel
25	chr2:112789000-112792600	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr2:112789000-112792600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr2:112789200-112790200	Enhancers	H1 Cell Line	embryonic stem cell
28	chr2:112789200-112790200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr2:112789200-112790200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr2:112789200-112790200	Enhancers	Brain Substantia Nigra	brain
31	chr2:112789200-112790800	Enhancers	Liver	Liver
32	chr2:112789200-112790800	Enhancers	Placenta	Placenta
33	chr2:112789200-112790800	Enhancers	Fetal Thymus	thymus
34	chr2:112789200-112790800	Flanking Active TSS	Dnd41	blood
35	chr2:112789200-112790800	Enhancers	HepG2	liver
36	chr2:112789200-112791400	Enhancers	Fetal Stomach	stomach
37	chr2:112789200-112791600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr2:112789200-112791600	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr2:112789200-112791600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr2:112789200-112791600	Enhancers	Brain Hippocampus Middle	brain
41	chr2:112789200-112791600	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr2:112789200-112792000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr2:112789200-112792000	Enhancers	Colon Smooth Muscle	Colon
44	chr2:112789400-112790200	Flanking Active TSS	NHEK	skin
45	chr2:112789400-112790800	Enhancers	GM12878-XiMat	blood
46	chr2:112789400-112791200	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
47	chr2:112789400-112791400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
48	chr2:112789600-112790200	Enhancers	H9 Cell Line	embryonic stem cell
49	chr2:112789600-112790800	Enhancers	Fetal Muscle Leg	muscle
50	chr2:112789600-112791000	Enhancers	Stomach Smooth Muscle	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links