Variant report

Variant	rs28416662
Chromosome Location	chr7:101386201-101386202
allele	G/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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:101383707..101389205-chr7:101455835..101460728,14	MCF-7	breast:
2	chr7:101370197..101372685-chr7:101384392..101387047,2	K562	blood:
3	chr7:101374945..101377549-chr7:101385778..101388199,3	K562	blood:
4	chr7:101386153..101388465-chr7:101446824..101448422,2	MCF-7	breast:
5	chr7:101383858..101388453-chr7:101455921..101461745,10	K562	blood:
6	chr7:101386120..101387098-chr7:101458652..101459478,4	MCF-7	breast:
7	chr7:101385593..101388435-chr7:101388835..101390401,2	K562	blood:
8	chr7:101375406..101379067-chr7:101385960..101390621,6	MCF-7	breast:
9	chr7:101374945..101377506-chr7:101385778..101388397,3	K562	blood:
10	chr7:101384444..101389414-chr7:101389757..101394090,5	MCF-7	breast:
11	chr7:101385593..101388435-chr7:101388835..101390929,3	K562	blood:
12	chr7:101358883..101362441-chr7:101383235..101387377,4	MCF-7	breast:
13	chr7:101381459..101384895-chr7:101386139..101388176,3	K562	blood:
14	chr7:101383224..101388686-chr7:101455921..101460973,10	K562	blood:
15	chr7:101386140..101387157-chr7:101458388..101459450,10	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000257923	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10228981	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10247290	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10258318	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11975225	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11977362	0.90[ASN][1000 genomes]
rs11977381	0.90[ASN][1000 genomes]
rs11984246	0.90[ASN][1000 genomes]
rs17135758	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28419515	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2906725	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2906726	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2906727	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2906728	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2906729	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2906730	0.96[ASN][1000 genomes]
rs2906731	0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2906736	0.93[ASN][1000 genomes]
rs2906737	0.86[ASN][1000 genomes]
rs2906738	0.89[ASN][1000 genomes]
rs2906739	0.89[ASN][1000 genomes]
rs2949324	0.89[ASN][1000 genomes]
rs2949325	0.89[ASN][1000 genomes]
rs2949326	0.89[ASN][1000 genomes]
rs2949327	0.89[ASN][1000 genomes]
rs2949329	0.93[ASN][1000 genomes]
rs2949332	0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2949333	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2949334	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2949335	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2949336	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2949337	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2970475	0.89[ASN][1000 genomes]
rs2970476	0.89[ASN][1000 genomes]
rs2970481	0.96[ASN][1000 genomes]
rs2970484	0.84[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2970485	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2970486	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2970487	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2970488	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2970490	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2970491	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2970492	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4354243	0.90[ASN][1000 genomes]
rs56024574	0.90[ASN][1000 genomes]
rs56257366	0.90[ASN][1000 genomes]
rs57730474	0.89[ASN][1000 genomes]
rs6975182	0.82[ASN][1000 genomes]
rs73400071	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9691113	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9691915	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933653	chr7:100701931-101515782	Active TSS ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv1018544	chr7:101225639-101424889	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv539045	chr7:101225639-101424889	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv482758	chr7:101231458-101395219	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv831079	chr7:101273495-101466776	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
6	nsv1021797	chr7:101342353-101466957	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv539046	chr7:101342353-101466957	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
8	nsv1024319	chr7:101368299-101668159	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
9	nsv539047	chr7:101368299-101668159	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:101377200-101386600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr7:101382800-101386600	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr7:101383000-101386400	Enhancers	Primary B cells from peripheral blood	blood
4	chr7:101383000-101386400	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr7:101383000-101386600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr7:101383000-101386600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr7:101383200-101386400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr7:101383200-101386600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr7:101383400-101386400	Weak transcription	A549	lung
10	chr7:101383400-101386400	Weak transcription	HMEC	breast
11	chr7:101383400-101386600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr7:101383400-101386600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr7:101383400-101386600	Weak transcription	Pancreas	Pancrea
14	chr7:101383400-101386600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr7:101384000-101386400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr7:101384000-101386400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr7:101384200-101386600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
18	chr7:101384200-101386600	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr7:101384600-101386400	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr7:101384600-101386600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr7:101384800-101386400	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr7:101384800-101386400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr7:101384800-101386400	Enhancers	Monocytes-CD14+_RO01746	blood
24	chr7:101384800-101386600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr7:101384800-101386600	Weak transcription	Gastric	stomach
26	chr7:101384800-101386600	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr7:101384800-101386600	Enhancers	GM12878-XiMat	blood
28	chr7:101384800-101386800	Weak transcription	Spleen	Spleen
29	chr7:101385400-101386400	Flanking Active TSS	Fetal Thymus	thymus
30	chr7:101385400-101386800	Flanking Active TSS	Dnd41	blood
31	chr7:101385600-101386400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
32	chr7:101385600-101386400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr7:101385600-101386400	Enhancers	Colonic Mucosa	Colon
34	chr7:101385600-101386400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
35	chr7:101385600-101386400	Weak transcription	Hela-S3	cervix
36	chr7:101385600-101388000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr7:101385800-101386400	Bivalent Enhancer	Fetal Stomach	stomach
38	chr7:101385800-101386400	Enhancers	K562	blood
39	chr7:101385800-101386600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr7:101385800-101386600	Flanking Active TSS	Primary hematopoietic stem cells	blood
41	chr7:101386000-101386400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr7:101386000-101386400	Bivalent Enhancer	Fetal Muscle Leg	muscle
43	chr7:101386000-101386600	Enhancers	Placenta	Placenta
44	chr7:101386000-101387400	Enhancers	Stomach Mucosa	stomach
45	chr7:101386200-101386400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
46	chr7:101386200-101386400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
47	chr7:101386200-101386400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr7:101386200-101386400	Weak transcription	Fetal Intestine Large	intestine
49	chr7:101386200-101386400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
50	chr7:101386200-101386400	Flanking Active TSS	Thymus	Thymus

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