Variant report

Variant	rs718312
Chromosome Location	chr2:39279413-39279414
allele	A/C/G/T
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	chr2:39279042-39279686	K562	blood:	n/a	n/a

Variant related genes	Relation type
SOS1	TF binding region

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10166557	1.00[EUR][1000 genomes]
rs10173380	1.00[EUR][1000 genomes]
rs10173563	1.00[EUR][1000 genomes]
rs10184046	1.00[EUR][1000 genomes]
rs10184855	1.00[EUR][1000 genomes]
rs10186842	1.00[EUR][1000 genomes]
rs10188701	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10189440	1.00[EUR][1000 genomes]
rs10194533	1.00[EUR][1000 genomes]
rs10196863	1.00[EUR][1000 genomes]
rs10199955	1.00[EUR][1000 genomes]
rs10202876	1.00[EUR][1000 genomes]
rs10203565	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10207187	1.00[EUR][1000 genomes]
rs10207984	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10495882	1.00[EUR][1000 genomes]
rs12329307	1.00[EUR][1000 genomes]
rs13387231	1.00[EUR][1000 genomes]
rs13394446	1.00[EUR][1000 genomes]
rs13395448	1.00[EUR][1000 genomes]
rs13407659	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13411756	1.00[EUR][1000 genomes]
rs13416725	1.00[EUR][1000 genomes]
rs13424493	1.00[EUR][1000 genomes]
rs13425165	1.00[EUR][1000 genomes]
rs13428418	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13432395	1.00[EUR][1000 genomes]
rs1451278	1.00[EUR][1000 genomes]
rs17023148	1.00[EUR][1000 genomes]
rs17023149	1.00[EUR][1000 genomes]
rs17023214	1.00[EUR][1000 genomes]
rs17023241	1.00[EUR][1000 genomes]
rs17023292	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1901290	1.00[EUR][1000 genomes]
rs2218850	1.00[EUR][1000 genomes]
rs2373466	1.00[EUR][1000 genomes]
rs2373472	1.00[EUR][1000 genomes]
rs3099938	1.00[EUR][1000 genomes]
rs3099953	1.00[EUR][1000 genomes]
rs3099997	1.00[EUR][1000 genomes]
rs3112160	1.00[EUR][1000 genomes]
rs3112164	1.00[EUR][1000 genomes]
rs3112174	1.00[EUR][1000 genomes]
rs3112177	1.00[EUR][1000 genomes]
rs55890805	1.00[EUR][1000 genomes]
rs56269328	1.00[EUR][1000 genomes]
rs56724744	1.00[EUR][1000 genomes]
rs57359008	1.00[EUR][1000 genomes]
rs59259697	1.00[EUR][1000 genomes]
rs60703378	1.00[EUR][1000 genomes]
rs61596046	1.00[EUR][1000 genomes]
rs6544200	1.00[EUR][1000 genomes]
rs6734212	1.00[EUR][1000 genomes]
rs6737680	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6751306	1.00[EUR][1000 genomes]
rs6753426	1.00[EUR][1000 genomes]
rs6754613	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs72906436	1.00[EUR][1000 genomes]
rs72906467	1.00[EUR][1000 genomes]
rs72916836	1.00[EUR][1000 genomes]
rs72916860	1.00[EUR][1000 genomes]
rs72918710	1.00[EUR][1000 genomes]
rs72925431	1.00[EUR][1000 genomes]
rs72925433	1.00[EUR][1000 genomes]
rs72925439	1.00[EUR][1000 genomes]
rs7340303	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73930506	1.00[EUR][1000 genomes]
rs7559586	1.00[EUR][1000 genomes]
rs7564481	1.00[EUR][1000 genomes]
rs7565814	1.00[EUR][1000 genomes]
rs7571608	1.00[EUR][1000 genomes]
rs7571719	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7574214	1.00[EUR][1000 genomes]
rs7582586	1.00[EUR][1000 genomes]
rs7589303	1.00[EUR][1000 genomes]
rs7599990	1.00[EUR][1000 genomes]
rs9646968	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873884	chr2:39154463-39332093	Genic enhancers Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv2755359	chr2:39169049-39417849	Strong transcription Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv873885	chr2:39200198-39573521	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1010874	chr2:39255376-39604535	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv535649	chr2:39255376-39604535	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv531346	chr2:39263225-39606367	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
7	nsv533348	chr2:39264345-39596169	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
8	nsv1014520	chr2:39270598-39596299	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
9	nsv535650	chr2:39270598-39596299	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
10	nsv1008198	chr2:39271472-39364035	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
11	nsv1009379	chr2:39271472-39604535	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
12	nsv581493	chr2:39277851-39547575	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
13	nsv581494	chr2:39277851-39626388	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39213800-39308000	Weak transcription	Pancreas	Pancrea
2	chr2:39227600-39303400	Weak transcription	Colonic Mucosa	Colon
3	chr2:39229800-39293000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:39232600-39300000	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:39235400-39312000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:39235600-39293200	Weak transcription	Fetal Brain Male	brain
7	chr2:39235600-39295800	Weak transcription	NHLF	lung
8	chr2:39235600-39298200	Weak transcription	Small Intestine	intestine
9	chr2:39235600-39327800	Weak transcription	Esophagus	oesophagus
10	chr2:39235800-39284000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr2:39235800-39293600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr2:39236000-39295600	Weak transcription	Aorta	Aorta
13	chr2:39236000-39295800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr2:39236000-39305600	Weak transcription	Gastric	stomach
15	chr2:39236200-39305600	Weak transcription	Lung	lung
16	chr2:39240800-39299200	Weak transcription	Brain Hippocampus Middle	brain
17	chr2:39241600-39292800	Weak transcription	GM12878-XiMat	blood
18	chr2:39243200-39299600	Weak transcription	Brain Substantia Nigra	brain
19	chr2:39244600-39295400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr2:39250000-39282200	Weak transcription	Brain Anterior Caudate	brain
21	chr2:39250000-39292800	Weak transcription	Psoas Muscle	Psoas
22	chr2:39250200-39295200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr2:39250200-39313600	Weak transcription	Brain Angular Gyrus	brain
24	chr2:39250400-39295600	Weak transcription	NH-A	brain
25	chr2:39250400-39303000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr2:39250600-39279800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr2:39251000-39293000	Weak transcription	HMEC	breast
28	chr2:39251600-39327200	Weak transcription	HUVEC	blood vessel
29	chr2:39252400-39292400	Weak transcription	NHEK	skin
30	chr2:39255000-39299000	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr2:39258200-39293400	Weak transcription	Ovary	ovary
32	chr2:39258400-39282600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr2:39258400-39292800	Weak transcription	HSMMtube	muscle
34	chr2:39258400-39295800	Weak transcription	Colon Smooth Muscle	Colon
35	chr2:39258400-39299200	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr2:39258400-39322400	Weak transcription	Thymus	Thymus
37	chr2:39259000-39293200	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr2:39260200-39293000	Weak transcription	Stomach Smooth Muscle	stomach
39	chr2:39260200-39295000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr2:39261000-39279600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:39261000-39279600	Weak transcription	Fetal Muscle Leg	muscle
42	chr2:39261000-39309800	Weak transcription	Spleen	Spleen
43	chr2:39261000-39318800	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr2:39261000-39327800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr2:39261600-39282000	Weak transcription	Osteobl	bone
46	chr2:39262000-39292600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr2:39270600-39284400	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr2:39270800-39280800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr2:39271400-39320400	Weak transcription	Right Ventricle	heart
50	chr2:39272200-39279600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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