Variant report

Variant	rs73952788
Chromosome Location	chr2:127729360-127729361
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:127728843..127730664-chr2:127736005..127737630,2	MCF-7	breast:
2	chr17:42421751..42423895-chr2:127728596..127731576,2	MCF-7	breast:
3	chr2:127285363..127286223-chr2:127729309..127730212,5	MCF-7	breast:
4	chr2:126503200..126503743-chr2:127729269..127730019,3	MCF-7	breast:
5	chr2:127643515..127644193-chr2:127729132..127729892,3	MCF-7	breast:
6	chr2:127534693..127535651-chr2:127729199..127730146,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000030582	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10168813	0.82[ASN][1000 genomes]
rs10803617	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10803618	0.86[ASN][1000 genomes]
rs12053575	0.86[ASN][1000 genomes]
rs12620265	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12692123	0.82[ASN][1000 genomes]
rs1553844	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1912498	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28758224	0.82[ASN][1000 genomes]
rs4662695	0.86[ASN][1000 genomes]
rs4662696	0.86[ASN][1000 genomes]
rs4662698	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4662699	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4663070	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4663075	0.86[ASN][1000 genomes]
rs4663076	0.86[ASN][1000 genomes]
rs4663077	0.86[ASN][1000 genomes]
rs4663079	0.86[ASN][1000 genomes]
rs4663080	0.86[ASN][1000 genomes]
rs4663081	0.86[ASN][1000 genomes]
rs4663082	0.86[ASN][1000 genomes]
rs4663083	0.86[ASN][1000 genomes]
rs55962144	0.94[ASN][1000 genomes]
rs61633215	0.92[ASN][1000 genomes]
rs6431201	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6431206	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6431207	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6431208	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6431209	0.86[ASN][1000 genomes]
rs6431210	0.86[ASN][1000 genomes]
rs6431211	0.92[ASN][1000 genomes]
rs6431212	0.92[ASN][1000 genomes]
rs6749935	0.86[ASN][1000 genomes]
rs6753685	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72976756	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72980845	0.92[ASN][1000 genomes]
rs72980853	1.00[EUR][1000 genomes]
rs72980861	1.00[EUR][1000 genomes]
rs73952789	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7419804	0.86[ASN][1000 genomes]
rs7420039	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7423317	0.86[ASN][1000 genomes]
rs7424763	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7556956	0.86[ASN][1000 genomes]
rs7557069	0.86[ASN][1000 genomes]
rs7565248	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7590060	0.82[ASN][1000 genomes]
rs870468	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9967839	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002265	chr2:127029745-127733458	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv535919	chr2:127029745-127733458	Strong transcription Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv999422	chr2:127464647-127956543	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv1004930	chr2:127477369-127938234	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv834365	chr2:127616996-127793863	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv834366	chr2:127633714-127784692	Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv3529164	chr2:127729086-127729400	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
8	esv3529163	chr2:127729160-127729442	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:127727800-127729400	Bivalent Enhancer	Fetal Stomach	stomach
2	chr2:127727800-127730600	Enhancers	Fetal Brain Male	brain
3	chr2:127728200-127729400	Bivalent Enhancer	Fetal Muscle Leg	muscle
4	chr2:127728200-127730200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:127728200-127730200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:127728400-127729400	Weak transcription	Fetal Brain Female	brain
7	chr2:127728600-127729400	Enhancers	Colon Smooth Muscle	Colon
8	chr2:127728600-127729400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
9	chr2:127728800-127729400	Active TSS	Liver	Liver
10	chr2:127728800-127729400	Active TSS	Brain Substantia Nigra	brain
11	chr2:127728800-127729600	Flanking Bivalent TSS/Enh	HepG2	liver
12	chr2:127728800-127729800	Active TSS	Brain Angular Gyrus	brain
13	chr2:127728800-127729800	Active TSS	Brain Cingulate Gyrus	brain
14	chr2:127728800-127730000	Enhancers	Lung	lung
15	chr2:127728800-127730000	Enhancers	Spleen	Spleen
16	chr2:127728800-127730200	Active TSS	Brain Anterior Caudate	brain
17	chr2:127729000-127729400	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr2:127729000-127729400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:127729000-127729400	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr2:127729000-127729400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
21	chr2:127729000-127729400	Bivalent/Poised TSS	HSMM	muscle
22	chr2:127729000-127729600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr2:127729000-127729600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr2:127729000-127729600	Bivalent/Poised TSS	A549	lung
25	chr2:127729000-127729800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
26	chr2:127729000-127729800	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
27	chr2:127729000-127729800	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr2:127729000-127729800	Active TSS	Aorta	Aorta
29	chr2:127729000-127729800	Active TSS	Pancreas	Pancrea
30	chr2:127729000-127729800	Active TSS	Rectal Mucosa Donor 29	rectum
31	chr2:127729000-127729800	Active TSS	K562	blood
32	chr2:127729000-127730000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
33	chr2:127729000-127730000	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
34	chr2:127729000-127730000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr2:127729000-127730000	Active TSS	Rectal Mucosa Donor 31	rectum
36	chr2:127729000-127730200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr2:127729200-127729400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr2:127729200-127729400	Active TSS	Primary monocytes fromperipheralblood	blood
39	chr2:127729200-127729400	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
40	chr2:127729200-127729400	Bivalent/Poised TSS	Primary T regulatory cells fromperipheralblood	blood
41	chr2:127729200-127729400	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
42	chr2:127729200-127729400	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr2:127729200-127729400	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
44	chr2:127729200-127729400	Active TSS	Brain Hippocampus Middle	brain
45	chr2:127729200-127729400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr2:127729200-127729400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr2:127729200-127729400	Active TSS	Fetal Intestine Large	intestine
48	chr2:127729200-127729400	Enhancers	Left Ventricle	heart
49	chr2:127729200-127729400	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
50	chr2:127729200-127729400	Bivalent/Poised TSS	Stomach Mucosa	stomach

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