Variant report

Variant	rs13425165
Chromosome Location	chr2:39334003-39334004
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39331060..39334578-chr2:39342620..39345134,3	K562	blood:
2	chr2:39332401..39334578-chr2:39342620..39345134,2	K562	blood:
3	chr2:39329508..39332372-chr2:39332776..39334374,2	MCF-7	breast:
4	chr2:39333333..39336921-chr2:39345551..39349571,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115904	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10166557	1.00[EUR][1000 genomes]
rs10173380	1.00[EUR][1000 genomes]
rs10173563	1.00[EUR][1000 genomes]
rs10184046	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10184855	1.00[EUR][1000 genomes]
rs10186842	1.00[EUR][1000 genomes]
rs10188701	1.00[EUR][1000 genomes]
rs10189440	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];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	1.00[EUR][1000 genomes]
rs10207187	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10207984	1.00[EUR][1000 genomes]
rs10495882	1.00[EUR][1000 genomes]
rs12329307	1.00[EUR][1000 genomes]
rs13387231	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13394446	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13395448	1.00[EUR][1000 genomes]
rs13407659	1.00[EUR][1000 genomes]
rs13411756	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13416725	1.00[EUR][1000 genomes]
rs13424493	1.00[EUR][1000 genomes]
rs13428418	1.00[EUR][1000 genomes]
rs13432395	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];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	1.00[EUR][1000 genomes]
rs297158	0.81[AFR][1000 genomes]
rs3112177	1.00[EUR][1000 genomes]
rs55890805	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56269328	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56724744	1.00[EUR][1000 genomes]
rs57359008	1.00[EUR][1000 genomes]
rs59259697	1.00[EUR][1000 genomes]
rs59732351	0.80[AFR][1000 genomes]
rs60031390	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs60703378	1.00[EUR][1000 genomes]
rs61596046	1.00[EUR][1000 genomes]
rs6544200	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6734212	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6737680	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6751306	1.00[EUR][1000 genomes]
rs6753426	1.00[EUR][1000 genomes]
rs6754613	1.00[EUR][1000 genomes]
rs718312	1.00[EUR][1000 genomes]
rs72906436	1.00[EUR][1000 genomes]
rs72906467	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72909662	0.81[AFR][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[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73930506	1.00[EUR][1000 genomes]
rs7559586	1.00[EUR][1000 genomes]
rs7564481	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7565814	1.00[EUR][1000 genomes]
rs7571608	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7571719	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7574214	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7582586	1.00[EUR][1000 genomes]
rs7589303	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7599990	1.00[EUR][1000 genomes]
rs9646968	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	nsv533456	chr2:39281834-39596298	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
14	nsv581495	chr2:39282079-39475205	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39280800-39334200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr2:39293800-39339400	Weak transcription	Fetal Muscle Trunk	muscle
3	chr2:39294000-39345200	Weak transcription	Fetal Kidney	kidney
4	chr2:39294600-39339400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr2:39296400-39339400	Weak transcription	Aorta	Aorta
6	chr2:39319600-39339600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:39319800-39343200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr2:39321000-39334200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:39321000-39334200	Weak transcription	Liver	Liver
10	chr2:39321000-39338600	Weak transcription	Duodenum Mucosa	Duodenum
11	chr2:39321000-39344600	Weak transcription	Gastric	stomach
12	chr2:39322400-39345200	Weak transcription	Osteobl	bone
13	chr2:39322600-39344400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr2:39322800-39334200	Weak transcription	Fetal Muscle Leg	muscle
15	chr2:39322800-39334200	Weak transcription	NHLF	lung
16	chr2:39322800-39334400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr2:39322800-39334400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr2:39322800-39334400	Weak transcription	K562	blood
19	chr2:39322800-39339200	Weak transcription	Fetal Thymus	thymus
20	chr2:39322800-39345200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr2:39323000-39334400	Weak transcription	Fetal Stomach	stomach
22	chr2:39323000-39339000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr2:39323000-39339400	Weak transcription	Primary hematopoietic stem cells	blood
24	chr2:39323000-39344800	Weak transcription	Primary T cells from cord blood	blood
25	chr2:39323200-39339400	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr2:39323200-39339400	Weak transcription	Fetal Intestine Large	intestine
27	chr2:39323400-39334600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr2:39323400-39339200	Weak transcription	Dnd41	blood
29	chr2:39323600-39337600	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr2:39325000-39335400	Weak transcription	Placenta	Placenta
31	chr2:39325000-39339400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr2:39326600-39338600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr2:39327000-39334400	Weak transcription	Fetal Brain Female	brain
34	chr2:39327000-39344600	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr2:39327600-39335200	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr2:39327800-39334600	Weak transcription	Fetal Heart	heart
37	chr2:39328000-39337600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr2:39328000-39339400	Weak transcription	Thymus	Thymus
39	chr2:39328000-39346800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr2:39328200-39337400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr2:39328200-39344600	Weak transcription	Hela-S3	cervix
42	chr2:39328400-39334200	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr2:39328400-39334800	Weak transcription	Colon Smooth Muscle	Colon
44	chr2:39328400-39335800	Weak transcription	Lung	lung
45	chr2:39328400-39339400	Weak transcription	Esophagus	oesophagus
46	chr2:39328600-39334200	Weak transcription	NHEK	skin
47	chr2:39328600-39334400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr2:39328600-39334400	Weak transcription	Left Ventricle	heart
49	chr2:39328600-39334400	Weak transcription	Right Atrium	heart
50	chr2:39328600-39339400	Weak transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links