Variant report

Variant	rs59896787
Chromosome Location	chr2:39657219-39657220
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39652451..39655493-chr2:39655687..39657617,3	K562	blood:
2	chr2:39637192..39639411-chr2:39655516..39658352,2	K562	blood:
3	chr2:39651403..39653951-chr2:39655387..39658790,4	K562	blood:
4	chr2:39655176..39658174-chr2:39672805..39675633,2	K562	blood:
5	chr2:39655304..39658022-chr2:39658367..39662517,3	K562	blood:
6	chr2:39654727..39657322-chr2:39662344..39664931,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000011566	Chromatin interaction
ENSG00000231312	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10490305	0.81[AFR][1000 genomes]
rs11886110	0.82[AFR][1000 genomes]
rs11886434	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11895366	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11898704	0.81[AFR][1000 genomes]
rs11902188	0.84[AFR][1000 genomes]
rs55750780	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55961227	0.85[AFR][1000 genomes]
rs56928728	0.82[AFR][1000 genomes]
rs57084694	1.00[AFR][1000 genomes]
rs58824151	0.85[AFR][1000 genomes]
rs60394429	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6544225	0.82[AFR][1000 genomes]
rs6712399	0.84[AFR][1000 genomes]
rs6723987	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6727395	0.84[AFR][1000 genomes]
rs6751506	0.84[AFR][1000 genomes]
rs73923887	0.85[AFR][1000 genomes]
rs73923888	0.85[AFR][1000 genomes]
rs73923889	0.85[AFR][1000 genomes]
rs73923895	0.81[AFR][1000 genomes]
rs73924011	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73924013	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73924016	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7565210	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7591563	0.82[AFR][1000 genomes]
rs7599017	0.84[AFR][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	esv1827292	chr2:39385155-39675339	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv1812828	chr2:39396457-39675339	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv2695	chr2:39643221-39688015	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39637200-39659000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr2:39639200-39658000	Weak transcription	Fetal Stomach	stomach
3	chr2:39640800-39660000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:39641200-39659600	Weak transcription	Brain Angular Gyrus	brain
5	chr2:39644200-39661600	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr2:39645000-39658800	Weak transcription	Brain Anterior Caudate	brain
7	chr2:39645200-39658200	Weak transcription	Right Ventricle	heart
8	chr2:39646000-39660200	Weak transcription	Fetal Intestine Small	intestine
9	chr2:39646200-39658000	Weak transcription	Liver	Liver
10	chr2:39647000-39657400	Weak transcription	Adipose Nuclei	Adipose
11	chr2:39647200-39658400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr2:39647200-39659000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr2:39647400-39657800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr2:39647400-39658400	Weak transcription	Small Intestine	intestine
15	chr2:39647400-39658600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr2:39647800-39660200	Weak transcription	Pancreas	Pancrea
17	chr2:39648400-39658200	Weak transcription	Aorta	Aorta
18	chr2:39649800-39659200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr2:39650000-39658600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr2:39651800-39658000	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr2:39652000-39658000	Weak transcription	Stomach Smooth Muscle	stomach
22	chr2:39652000-39658600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr2:39652000-39662400	Weak transcription	Esophagus	oesophagus
24	chr2:39652000-39662400	Weak transcription	Lung	lung
25	chr2:39652200-39658000	Weak transcription	GM12878-XiMat	blood
26	chr2:39652400-39661200	Weak transcription	HUVEC	blood vessel
27	chr2:39652800-39657800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr2:39652800-39658000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr2:39652800-39658200	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr2:39652800-39658200	Weak transcription	Hela-S3	cervix
31	chr2:39652800-39658600	Weak transcription	Left Ventricle	heart
32	chr2:39652800-39658600	Weak transcription	Right Atrium	heart
33	chr2:39652800-39659000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr2:39652800-39660200	Weak transcription	Ovary	ovary
35	chr2:39652800-39661400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr2:39652800-39661400	Weak transcription	Primary hematopoietic stem cells	blood
37	chr2:39652800-39661600	Weak transcription	Fetal Thymus	thymus
38	chr2:39653000-39658200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr2:39653200-39658000	Weak transcription	HSMMtube	muscle
40	chr2:39653400-39658000	Weak transcription	HSMM	muscle
41	chr2:39653400-39658000	Weak transcription	NHLF	lung
42	chr2:39653400-39658200	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr2:39653600-39658600	Weak transcription	Stomach Mucosa	stomach
44	chr2:39653800-39657600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr2:39654000-39659800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr2:39654400-39660400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr2:39654800-39657800	Weak transcription	Colon Smooth Muscle	Colon
48	chr2:39654800-39658200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr2:39654800-39658400	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr2:39654800-39658600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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