Variant report

Variant	rs2120061
Chromosome Location	chr13:76387506-76387507
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	GATA2	chr13:76386856-76387904	SH-SY5Y	brain:	n/a	chr13:76387125-76387133 chr13:76387097-76387107 chr13:76387297-76387306 chr13:76387294-76387310
2	EP300	chr13:76386480-76387959	SK-N-SH	brain:	n/a	chr13:76387448-76387458 chr13:76386716-76386725 chr13:76386832-76386846
3	POLR2A	chr13:76387184-76387869	HepG2	liver:	n/a	n/a
4	GATA3	chr13:76386660-76387577	SK-N-SH	brain:	n/a	chr13:76387125-76387133 chr13:76387097-76387107 chr13:76387297-76387306 chr13:76387294-76387310
5	GATA3	chr13:76386749-76387533	SK-N-SH	brain:	n/a	chr13:76387125-76387133 chr13:76387097-76387107 chr13:76387297-76387306 chr13:76387294-76387310

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:76386406..76389041-chr13:76432929..76434756,2	MCF-7	breast:

Variant related genes	Relation type
LMO7	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs12427729	1.00[ASW][hapmap];0.81[CHD][hapmap];0.86[MEX][hapmap]
rs12428617	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12429534	0.90[ASN][1000 genomes]
rs12430034	0.84[ASN][1000 genomes]
rs12430940	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17065053	0.85[ASN][1000 genomes]
rs17065074	0.97[ASN][1000 genomes]
rs17065145	0.85[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2120060	0.83[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];0.85[JPT][hapmap];0.92[MKK][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2241913	0.97[ASN][1000 genomes]
rs2296093	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3736858	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3759445	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3783025	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3825439	0.84[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41287008	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58447742	0.82[ASN][1000 genomes]
rs61958156	0.82[ASN][1000 genomes]
rs61959560	0.84[ASN][1000 genomes]
rs61959561	0.85[ASN][1000 genomes]
rs61959583	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs629443	0.93[ASN][1000 genomes]
rs9318380	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9530471	0.85[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9544047	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9544049	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9544050	0.92[CHB][hapmap];0.92[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9544051	0.85[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9544053	0.84[ASN][1000 genomes]
rs9544056	0.85[CHB][hapmap]
rs9544059	1.00[ASW][hapmap];0.84[CHD][hapmap];0.81[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832646	chr13:76300428-76483102	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	esv2758333	chr13:76321610-76542003	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats 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	9 gene(s)	inside rSNPs	diseases
3	esv2759950	chr13:76321610-76542003	Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76361600-76397800	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr13:76370400-76415600	Weak transcription	Primary B cells from cord blood	blood
3	chr13:76373000-76414600	Weak transcription	HMEC	breast
4	chr13:76376800-76415400	Weak transcription	Stomach Smooth Muscle	stomach
5	chr13:76377400-76395000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr13:76377600-76395200	Weak transcription	GM12878-XiMat	blood
7	chr13:76377600-76398600	Weak transcription	Primary B cells from peripheral blood	blood
8	chr13:76377600-76415800	Weak transcription	Dnd41	blood
9	chr13:76377600-76416200	Weak transcription	A549	lung
10	chr13:76378200-76397800	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr13:76378200-76415800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr13:76378400-76392200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr13:76378400-76415600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr13:76378800-76393200	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr13:76379200-76394800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr13:76380600-76388600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr13:76380600-76395200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr13:76380600-76397800	Weak transcription	Colonic Mucosa	Colon
19	chr13:76380600-76397800	Weak transcription	Fetal Muscle Trunk	muscle
20	chr13:76380600-76398000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr13:76380600-76400400	Weak transcription	Esophagus	oesophagus
22	chr13:76380600-76405600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr13:76380800-76391200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr13:76380800-76392800	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr13:76380800-76397800	Weak transcription	Brain Anterior Caudate	brain
26	chr13:76381000-76392400	Weak transcription	Duodenum Mucosa	Duodenum
27	chr13:76382400-76387600	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr13:76382400-76388400	Weak transcription	Fetal Muscle Leg	muscle
29	chr13:76382400-76391000	Weak transcription	Liver	Liver
30	chr13:76382400-76392400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr13:76382400-76392400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr13:76382400-76392400	Weak transcription	NHLF	lung
33	chr13:76382600-76387600	Weak transcription	Left Ventricle	heart
34	chr13:76382600-76392400	Weak transcription	Fetal Intestine Small	intestine
35	chr13:76382800-76391400	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr13:76383200-76391400	Weak transcription	NH-A	brain
37	chr13:76384000-76389200	Enhancers	Fetal Thymus	thymus
38	chr13:76384200-76390600	Genic enhancers	Osteobl	bone
39	chr13:76384600-76390400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr13:76385200-76387600	Weak transcription	Primary T cells from cord blood	blood
41	chr13:76385800-76387600	Enhancers	Thymus	Thymus
42	chr13:76385800-76387800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr13:76385800-76388400	Weak transcription	Right Atrium	heart
44	chr13:76385800-76389400	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr13:76385800-76391200	Weak transcription	Hela-S3	cervix
46	chr13:76386000-76388400	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr13:76386200-76387800	Enhancers	Fetal Stomach	stomach
48	chr13:76386200-76388000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr13:76386200-76388000	Enhancers	Fetal Brain Female	brain
50	chr13:76386200-76388000	Enhancers	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links