Variant report

Variant	rs12701787
Chromosome Location	chr7:39994122-39994123
allele	C/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	POLR2A	chr7:39993725-39994918	GM12878	blood:	n/a	n/a
2	CHD1	chr7:39994009-39994176	GM12878	blood:	n/a	n/a
3	POLR2A	chr7:39994091-39994226	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:39992254..39999333-chr7:39999543..40002599,8	K562	blood:
2	chr7:39992705..39994767-chr7:40040920..40043283,2	K562	blood:
3	chr7:39992179..39995720-chr7:40011134..40014847,3	K562	blood:
4	chr7:39993833..39995767-chr7:39996251..39998539,2	MCF-7	breast:
5	chr7:39991743..39994324-chr7:40009939..40012634,2	K562	blood:

Variant related genes	Relation type
ENSG00000259826	TF binding region

Extended variants
information (count: 56 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10046564	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10224206	0.95[EUR][1000 genomes]
rs10225492	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10235989	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10239324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10247292	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10253590	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10272514	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10277853	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10279016	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1082023	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13231977	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13239106	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13241453	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13310449	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13310480	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17434388	0.82[EUR][1000 genomes]
rs17435812	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17496226	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17496247	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17526699	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2140254	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2329611	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28492942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28547436	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28638437	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34326687	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34470312	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34748607	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35052806	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35082351	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35226291	0.81[EUR][1000 genomes]
rs35618050	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4273753	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4428576	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4481477	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4498451	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6947071	0.83[EUR][1000 genomes]
rs73127832	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73127862	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs773382	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7780996	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7794792	0.81[EUR][1000 genomes]
rs7811585	0.81[EUR][1000 genomes]
rs809558	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs878785	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9639817	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9639820	0.97[EUR][1000 genomes]
rs9655407	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9690347	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9986996	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9986997	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv887973	chr7:39772654-40110720	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
2	nsv887975	chr7:39858378-40124137	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
3	nsv887976	chr7:39874986-40018693	Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
4	nsv887977	chr7:39885541-40018693	ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39988200-39996200	Active TSS	GM12878-XiMat	blood
2	chr7:39988400-39994200	Active TSS	NHLF	lung
3	chr7:39991400-39994200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
4	chr7:39991400-39994200	Active TSS	Right Atrium	heart
5	chr7:39991400-39994600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr7:39991600-39994400	Weak transcription	Spleen	Spleen
7	chr7:39991800-39994400	Weak transcription	Pancreas	Pancrea
8	chr7:39991800-39994600	Weak transcription	Gastric	stomach
9	chr7:39991800-39996200	Weak transcription	Esophagus	oesophagus
10	chr7:39991800-40000200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr7:39991800-40000800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr7:39991800-40005200	Weak transcription	Lung	lung
13	chr7:39992000-39994800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr7:39992000-39999200	Weak transcription	Fetal Muscle Trunk	muscle
15	chr7:39992000-40006400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr7:39992400-39994200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr7:39992400-39994800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr7:39992400-39995600	Flanking Active TSS	Dnd41	blood
19	chr7:39992600-40001200	Weak transcription	Placenta	Placenta
20	chr7:39993000-39994200	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr7:39993000-39995000	Enhancers	Fetal Stomach	stomach
22	chr7:39993000-39995200	Enhancers	Primary neutrophils fromperipheralblood	blood
23	chr7:39993000-39995200	Enhancers	Brain Substantia Nigra	brain
24	chr7:39993200-39994400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr7:39993200-39994400	Weak transcription	Fetal Muscle Leg	muscle
26	chr7:39993200-39994600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr7:39993200-39995000	Transcr. at gene 5' and 3'	K562	blood
28	chr7:39993200-39995200	Enhancers	Small Intestine	intestine
29	chr7:39993200-39997200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr7:39993400-39994200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr7:39993400-39994200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr7:39993400-39994200	Flanking Active TSS	Osteobl	bone
33	chr7:39993400-39994600	Weak transcription	Aorta	Aorta
34	chr7:39993400-39994800	Enhancers	Fetal Intestine Large	intestine
35	chr7:39993400-39995000	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr7:39993400-39995000	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr7:39993400-39995400	Enhancers	Primary B cells from peripheral blood	blood
38	chr7:39993400-40000000	Weak transcription	Fetal Thymus	thymus
39	chr7:39993400-40001000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr7:39993600-39994200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr7:39993600-39994200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr7:39993600-39994200	Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr7:39993600-39994200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr7:39993600-39994200	Active TSS	HSMM	muscle
45	chr7:39993600-39994400	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr7:39993600-39994400	Enhancers	Fetal Lung	lung
47	chr7:39993600-39994400	Active TSS	Ovary	ovary
48	chr7:39993600-39994400	Enhancers	A549	lung
49	chr7:39993600-39994600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr7:39993600-39994600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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