Variant report

Variant	rs12539310
Chromosome Location	chr7:101526779-101526780
allele	A/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:31)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:31 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:101526331..101527126-chr7:101647167..101647819,3	MCF-7	breast:
2	chr7:101526222..101527789-chr7:101530737..101532472,2	K562	blood:
3	chr7:101524538..101530208-chr7:101583819..101590225,13	MCF-7	breast:
4	chr7:101526287..101527935-chr7:101528596..101530450,2	K562	blood:
5	chr7:101522402..101527695-chr7:101541882..101547914,5	MCF-7	breast:
6	chr7:101500051..101501733-chr7:101526046..101528456,2	K562	blood:
7	chr7:101514608..101516122-chr7:101525582..101528029,2	K562	blood:
8	chr7:101524859..101527642-chr7:101545155..101548859,4	K562	blood:
9	chr7:101498446..101503068-chr7:101525023..101527426,4	MCF-7	breast:
10	chr7:101486111..101487639-chr7:101525637..101527848,2	K562	blood:
11	chr7:101526289..101528067-chr7:101530737..101533297,2	K562	blood:
12	chr7:101512083..101520283-chr7:101521327..101527237,12	K562	blood:
13	chr7:101457345..101464020-chr7:101524379..101528846,10	MCF-7	breast:
14	chr7:101526158..101527020-chr7:101615774..101616664,2	MCF-7	breast:
15	chr7:101485853..101487639-chr7:101524397..101527137,2	K562	blood:
16	chr7:101526306..101527124-chr7:101615659..101616592,2	MCF-7	breast:
17	chr7:101524415..101527254-chr7:101635329..101637588,2	MCF-7	breast:
18	chr7:101512554..101516171-chr7:101524650..101528130,5	MCF-7	breast:
19	chr7:101526144..101529822-chr7:101529905..101534800,8	MCF-7	breast:
20	chr7:101526260..101527081-chr7:101554377..101555031,2	MCF-7	breast:
21	chr7:101525676..101527121-chr7:101647199..101648097,5	MCF-7	breast:
22	chr7:101456951..101464631-chr7:101524079..101528885,15	MCF-7	breast:
23	chr7:101526412..101529161-chr7:101615489..101617394,2	MCF-7	breast:
24	chr7:101524980..101528234-chr7:101584443..101587218,5	MCF-7	breast:
25	chr7:101504130..101506941-chr7:101522541..101527065,4	K562	blood:
26	chr7:101524654..101529313-chr7:101536956..101539660,5	MCF-7	breast:
27	chr7:101525862..101528715-chr7:101557017..101559763,2	MCF-7	breast:
28	chr7:101524926..101527642-chr7:101546281..101548486,3	K562	blood:
29	chr7:101525260..101527111-chr7:101652933..101654478,2	MCF-7	breast:
30	chr7:101525890..101527612-chr7:101531987..101533703,2	MCF-7	breast:
31	chr7:101526018..101527121-chr7:101647260..101648089,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000257923	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10081174	0.82[AMR][1000 genomes]
rs10226289	0.88[CEU][hapmap];0.84[AMR][1000 genomes]
rs10227516	0.88[CEU][hapmap];0.92[MEX][hapmap];0.88[AMR][1000 genomes]
rs10241905	0.88[CEU][hapmap];0.84[GIH][hapmap];0.84[MEX][hapmap];0.81[AMR][1000 genomes]
rs10242019	1.00[ASW][hapmap];0.88[CEU][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs10255356	0.84[AMR][1000 genomes]
rs10256232	0.88[CEU][hapmap];0.84[AMR][1000 genomes]
rs10259103	0.81[AMR][1000 genomes]
rs10259964	0.88[CEU][hapmap];0.84[AMR][1000 genomes]
rs10261524	0.81[AMR][1000 genomes]
rs10261568	0.84[JPT][hapmap]
rs10264844	0.88[CEU][hapmap];0.84[AMR][1000 genomes]
rs10264855	0.84[AMR][1000 genomes]
rs10264866	0.88[CEU][hapmap];0.84[MEX][hapmap];0.84[AMR][1000 genomes]
rs10271171	0.84[AMR][1000 genomes]
rs10271610	0.88[CEU][hapmap];0.82[AMR][1000 genomes]
rs10271838	0.85[CEU][hapmap];0.82[AMR][1000 genomes]
rs10275899	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10279763	0.88[CEU][hapmap];0.84[MEX][hapmap];0.82[AMR][1000 genomes]
rs12532535	0.89[AMR][1000 genomes]
rs12534641	0.84[AMR][1000 genomes]
rs13227531	0.88[CEU][hapmap];0.84[AMR][1000 genomes]
rs13229243	0.82[AMR][1000 genomes]
rs13236072	0.91[ASW][hapmap];0.88[CEU][hapmap];0.85[LWK][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs13238593	0.86[TSI][hapmap]
rs13241079	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2410921	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28409703	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34750675	0.92[AMR][1000 genomes]
rs35065711	0.81[AMR][1000 genomes]
rs4729756	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4729757	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4729759	0.88[CEU][hapmap];0.84[MEX][hapmap];0.84[AMR][1000 genomes]
rs4729760	0.88[CEU][hapmap];0.84[MEX][hapmap];0.82[AMR][1000 genomes]
rs55824493	0.81[AMR][1000 genomes]
rs60656667	0.89[AMR][1000 genomes]
rs72603509	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72603510	0.92[AMR][1000 genomes]
rs72603511	0.82[AMR][1000 genomes]
rs72603512	0.89[AMR][1000 genomes]
rs9656073	0.83[AMR][1000 genomes]

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	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
2	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
3	nsv1020372	chr7:101420819-101718950	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:101514400-101527400	Weak transcription	GM12878-XiMat	blood
2	chr7:101521200-101526800	Enhancers	Fetal Intestine Large	intestine
3	chr7:101521200-101527000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr7:101521200-101527600	Enhancers	Placenta	Placenta
5	chr7:101521200-101528800	Enhancers	Fetal Heart	heart
6	chr7:101521600-101527600	Weak transcription	Gastric	stomach
7	chr7:101521800-101527000	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr7:101523000-101526800	Enhancers	Brain Germinal Matrix	brain
9	chr7:101523000-101527000	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr7:101523200-101543200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr7:101523600-101527000	Enhancers	Stomach Mucosa	stomach
12	chr7:101523600-101527600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr7:101523600-101528000	Enhancers	Duodenum Mucosa	Duodenum
14	chr7:101523600-101528600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr7:101523600-101529400	Enhancers	Rectal Mucosa Donor 29	rectum
16	chr7:101523600-101529600	Enhancers	Rectal Smooth Muscle	rectum
17	chr7:101524000-101526800	Enhancers	NHLF	lung
18	chr7:101524000-101527600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr7:101524000-101527600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr7:101524000-101527600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr7:101524400-101526800	Genic enhancers	Fetal Intestine Small	intestine
22	chr7:101524400-101527200	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr7:101524400-101527400	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr7:101524400-101527800	Weak transcription	Thymus	Thymus
25	chr7:101524600-101527200	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr7:101524600-101527400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr7:101524800-101527600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr7:101524800-101528200	Weak transcription	Right Ventricle	heart
29	chr7:101525000-101527600	Weak transcription	Primary T cells from cord blood	blood
30	chr7:101525000-101527600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr7:101525200-101527400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr7:101525400-101527000	Enhancers	Fetal Muscle Leg	muscle
33	chr7:101525400-101528000	Enhancers	Primary neutrophils fromperipheralblood	blood
34	chr7:101525600-101526800	Enhancers	Small Intestine	intestine
35	chr7:101525600-101526800	Flanking Active TSS	Stomach Smooth Muscle	stomach
36	chr7:101525600-101527000	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr7:101525600-101527000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr7:101525600-101527000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr7:101525600-101527000	Enhancers	iPS-18 Cell Line	embryonic stem cell
40	chr7:101525600-101527000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr7:101525600-101527000	Enhancers	Fetal Lung	lung
42	chr7:101525800-101526800	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr7:101525800-101526800	Flanking Active TSS	HUVEC	blood vessel
44	chr7:101525800-101526800	Flanking Active TSS	K562	blood
45	chr7:101525800-101527000	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr7:101525800-101527000	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr7:101525800-101527000	Enhancers	Fetal Stomach	stomach
48	chr7:101526000-101526800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
49	chr7:101526000-101528800	Enhancers	Dnd41	blood
50	chr7:101526000-101530200	Enhancers	Fetal Thymus	thymus

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