Variant report

Variant	rs10259773
Chromosome Location	chr7:5741099-5741100
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:5734503..5737746-chr7:5737831..5742522,7	MCF-7	breast:
2	chr7:5731961..5734457-chr7:5739866..5742131,3	MCF-7	breast:
3	chr7:5740407..5742553-chr7:5742668..5744217,2	K562	blood:
4	chr7:5740535..5742233-chr7:5749544..5751969,2	K562	blood:
5	chr7:5729527..5732207-chr7:5738007..5741204,4	K562	blood:
6	chr7:5739854..5741954-chr7:5752710..5755098,3	K562	blood:
7	chr7:5739854..5741954-chr7:5752710..5755970,3	K562	blood:
8	chr7:5738793..5741830-chr7:5758066..5760879,3	K562	blood:
9	chr7:5732704..5734919-chr7:5739330..5741424,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000011275	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10232762	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10233615	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10241310	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10275238	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1035331	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11531468	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12531598	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1990836	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2009260	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2287593	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2287595	0.94[ASN][1000 genomes]
rs2345938	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs3735289	0.94[ASN][1000 genomes]
rs3801016	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3801019	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3823683	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4720640	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4720641	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4720642	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4724713	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4724718	0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs61203027	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6463506	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6463507	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6944143	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6956960	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6958272	0.85[AMR][1000 genomes]
rs6960381	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6960897	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7777831	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7796461	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7800691	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7803308	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs852257	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs852258	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs852265	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs852266	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs852267	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs852375	0.83[EUR][1000 genomes]
rs852376	0.83[EUR][1000 genomes]
rs852397	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs852402	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs852409	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs852410	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs852415	0.87[AFR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs852420	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs852421	0.83[EUR][1000 genomes]
rs852468	0.83[EUR][1000 genomes]
rs852516	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs888582	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs888583	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9648578	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869165	chr7:4889618-5799719	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	352 gene(s)	inside rSNPs	diseases
2	nsv530979	chr7:5101631-5864814	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
3	nsv530981	chr7:5157150-5920006	Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	348 gene(s)	inside rSNPs	diseases
4	nsv530983	chr7:5370746-6070852	Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	368 gene(s)	inside rSNPs	diseases
5	nsv916391	chr7:5417945-5889565	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	336 gene(s)	inside rSNPs	diseases
6	nsv533108	chr7:5488018-6316581	Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	390 gene(s)	inside rSNPs	diseases
7	nsv482449	chr7:5557585-5743673	Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
8	nsv1033556	chr7:5565080-6186815	Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
9	nsv538710	chr7:5565080-6186815	Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
10	nsv530467	chr7:5617816-5815082	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
11	nsv1017612	chr7:5629728-5819144	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
12	nsv1021989	chr7:5629728-6186815	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers 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 miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
13	nsv887417	chr7:5667645-5760860	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
14	nsv887418	chr7:5675305-5772551	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
15	nsv887419	chr7:5703669-5820383	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
16	nsv1028652	chr7:5706207-5769489	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
17	nsv830891	chr7:5726301-5895460	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:5720200-5741400	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr7:5723400-5766400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr7:5732600-5747600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr7:5734200-5743400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr7:5735400-5741800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr7:5735600-5742000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr7:5735600-5742000	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr7:5735600-5742000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr7:5735800-5741400	Genic enhancers	Fetal Thymus	thymus
10	chr7:5735800-5741800	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr7:5735800-5742000	Enhancers	Primary T cells fromperipheralblood	blood
12	chr7:5735800-5744200	Enhancers	Brain Angular Gyrus	brain
13	chr7:5735800-5744200	Enhancers	Brain Anterior Caudate	brain
14	chr7:5735800-5746000	Weak transcription	HUVEC	blood vessel
15	chr7:5736400-5742400	Weak transcription	Fetal Brain Male	brain
16	chr7:5736800-5741200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr7:5737200-5743200	Enhancers	Brain Substantia Nigra	brain
18	chr7:5737200-5748400	Weak transcription	Colonic Mucosa	Colon
19	chr7:5737400-5767200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr7:5737600-5774200	Strong transcription	Dnd41	blood
21	chr7:5738000-5741600	Enhancers	Thymus	Thymus
22	chr7:5738000-5748200	Weak transcription	Small Intestine	intestine
23	chr7:5738600-5741200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr7:5738800-5741200	Flanking Active TSS	GM12878-XiMat	blood
25	chr7:5738800-5741400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
26	chr7:5738800-5742600	Enhancers	Pancreatic Islets	Pancreatic Islet
27	chr7:5739200-5741200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr7:5739200-5741200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
29	chr7:5739200-5741400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr7:5739200-5741400	Enhancers	Right Ventricle	heart
31	chr7:5739200-5741400	Genic enhancers	Monocytes-CD14+_RO01746	blood
32	chr7:5739200-5741600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr7:5739200-5741800	Genic enhancers	Left Ventricle	heart
34	chr7:5739200-5743000	Strong transcription	Liver	Liver
35	chr7:5739200-5744000	Genic enhancers	A549	lung
36	chr7:5739400-5741200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr7:5739400-5741200	Genic enhancers	NH-A	brain
38	chr7:5739400-5742200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr7:5739600-5741400	Enhancers	Brain Hippocampus Middle	brain
40	chr7:5739600-5742000	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr7:5739600-5743200	Strong transcription	Lung	lung
42	chr7:5739600-5743400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr7:5739600-5769600	Strong transcription	Fetal Intestine Large	intestine
44	chr7:5739800-5741200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
45	chr7:5739800-5741400	Enhancers	Primary neutrophils fromperipheralblood	blood
46	chr7:5739800-5741400	Weak transcription	Brain Germinal Matrix	brain
47	chr7:5739800-5741600	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr7:5739800-5741600	Genic enhancers	NHEK	skin
49	chr7:5739800-5742400	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr7:5739800-5742400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links