Variant report

Variant	rs28362379
Chromosome Location	chr2:10587234-10587235
allele	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	CHD1	chr2:10586760-10588522	GM12878	blood:	n/a	n/a
2	POLR2A	chr2:10586448-10590304	IMR90	lung:	n/a	n/a
3	MXI1	chr2:10586728-10589490	K562	blood:	n/a	chr2:10588938-10588947 chr2:10588938-10588947 chr2:10588127-10588136 chr2:10588940-10588949 chr2:10588494-10588509 chr2:10588496-10588511 chr2:10588125-10588134
4	CHD1	chr2:10586355-10588647	IMR90	lung:	n/a	n/a
5	TBL1XR1	chr2:10586926-10587888	K562	blood:	n/a	n/a
6	TAL1	chr2:10586579-10589021	K562	blood:	n/a	n/a
7	MYC	chr2:10586915-10590561	A549	lung:	n/a	chr2:10588126-10588135 chr2:10588941-10588950 chr2:10588939-10588948 chr2:10588651-10588660 chr2:10588126-10588136 chr2:10588125-10588136 chr2:10588939-10588949 chr2:10588496-10588505 chr2:10588124-10588137 chr2:10588938-10588949 chr2:10589691-10589701 chr2:10588125-10588134 chr2:10588938-10588948 chr2:10588125-10588136 chr2:10588938-10588949 chr2:10588930-10588946 chr2:10588939-10588948 chr2:10588500-10588509 chr2:10588125-10588136 chr2:10588124-10588137 chr2:10588939-10588948
8	JUN	chr2:10587119-10590477	K562	blood:	n/a	chr2:10590266-10590279 chr2:10588361-10588370
9	MXI1	chr2:10586524-10589700	SK-N-SH	brain:	n/a	chr2:10588938-10588947 chr2:10588938-10588947 chr2:10588127-10588136 chr2:10588940-10588949 chr2:10588494-10588509 chr2:10588496-10588511 chr2:10588125-10588134
10	TBP	chr2:10587206-10587848	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr2:10586318-10590638	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr2:10586617-10589143	MCF10A-Er-Src	breast:	n/a	n/a
13	MXI1	chr2:10586568-10589541	IMR90	lung:	n/a	chr2:10588938-10588947 chr2:10588938-10588947 chr2:10588127-10588136 chr2:10588940-10588949 chr2:10588494-10588509 chr2:10588496-10588511 chr2:10588125-10588134
14	CUX1	chr2:10587144-10587510	GM12878	blood:	n/a	n/a
15	POLR2A	chr2:10586686-10589014	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:10259653..10265917-chr2:10585320..10590295,8	MCF-7	breast:
2	chr2:10586529..10589550-chr2:10592115..10595368,3	MCF-7	breast:
3	chr2:10420712..10423243-chr2:10586890..10589076,2	K562	blood:
4	chr2:10441623..10444200-chr2:10586906..10588748,2	K562	blood:
5	chr2:10441623..10444177-chr2:10587166..10588748,2	K562	blood:
6	chr2:10259839..10264771-chr2:10582056..10590038,19	K562	blood:
7	chr2:10584788..10589777-chr2:10826863..10830293,6	K562	blood:
8	chr2:10259710..10265084-chr2:10586364..10590442,7	MCF-7	breast:
9	chr2:10265245..10266788-chr2:10587089..10589177,2	K562	blood:
10	chr2:10191630..10196148-chr2:10586386..10589794,5	K562	blood:
11	chr2:10257984..10265070-chr2:10582045..10589780,17	K562	blood:
12	chr2:9982517..9985169-chr2:10586715..10588876,2	K562	blood:
13	chr2:10587002..10587961-chr9:130548122..130548787,2	Hela-S3	cervix:

Variant related genes	Relation type
SNORA80B	TF binding region
ENSG00000257135	TF binding region
ENSG00000264030	Chromatin interaction
ENSG00000271787	Chromatin interaction
ENSG00000272524	Chromatin interaction
ENSG00000115761	Chromatin interaction
ENSG00000171848	Chromatin interaction
ENSG00000115756	Chromatin interaction
ENSG00000136807	Chromatin interaction
ENSG00000217258	Chromatin interaction
ENSG00000115750	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10164910	1.00[AMR][1000 genomes]
rs10490728	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11903106	1.00[ASN][1000 genomes]
rs11904157	1.00[ASN][1000 genomes]
rs13395781	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530829	chr2:10357105-10655131	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
2	nsv873645	chr2:10537347-10612091	Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
3	nsv1007185	chr2:10540386-10791743	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv873646	chr2:10550517-10612091	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
5	esv1840383	chr2:10569021-10588903	Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
6	nsv873647	chr2:10576424-10597858	Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
7	nsv873648	chr2:10584639-10599493	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
8	esv1819730	chr2:10585164-10591407	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
9	esv1818042	chr2:10585364-10591407	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
10	esv1840643	chr2:10585364-10607465	Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
11	nsv873649	chr2:10585458-10591628	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
12	nsv873650	chr2:10585458-10597858	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
13	nsv873651	chr2:10585575-10597858	Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
14	esv1792409	chr2:10585687-10588600	Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
15	esv1835530	chr2:10585687-10591407	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
16	nsv580963	chr2:10586780-10588903	Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10573000-10587400	Weak transcription	Right Atrium	heart
2	chr2:10577200-10587800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr2:10580000-10587400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:10580000-10587400	Weak transcription	Stomach Mucosa	stomach
5	chr2:10582600-10587400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr2:10584600-10587600	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr2:10584800-10587400	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr2:10584800-10587400	Weak transcription	Pancreas	Pancrea
9	chr2:10585000-10587400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr2:10585000-10587400	Weak transcription	Ovary	ovary
11	chr2:10585000-10587400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr2:10585000-10587400	Weak transcription	Right Ventricle	heart
13	chr2:10585000-10587600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:10585000-10587600	Weak transcription	Esophagus	oesophagus
15	chr2:10585000-10587600	Transcr. at gene 5' and 3'	NHEK	skin
16	chr2:10585000-10587800	Weak transcription	Spleen	Spleen
17	chr2:10585200-10587400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr2:10585200-10587400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr2:10585200-10587400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr2:10585200-10587800	Flanking Active TSS	Primary B cells from peripheral blood	blood
21	chr2:10585200-10588000	Flanking Active TSS	Primary B cells from cord blood	blood
22	chr2:10585400-10587400	Enhancers	Brain Hippocampus Middle	brain
23	chr2:10585600-10587400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr2:10585600-10588000	Active TSS	Fetal Kidney	kidney
25	chr2:10585600-10589000	Active TSS	GM12878-XiMat	blood
26	chr2:10585800-10587400	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr2:10586000-10587400	Enhancers	Primary hematopoietic stem cells	blood
28	chr2:10586000-10587400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr2:10586000-10589600	Active TSS	Pancreatic Islets	Pancreatic Islet
30	chr2:10586200-10587400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr2:10586200-10587800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr2:10586200-10588200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr2:10586200-10588800	Active TSS	Fetal Muscle Trunk	muscle
34	chr2:10586200-10589000	Active TSS	HSMM	muscle
35	chr2:10586200-10589000	Active TSS	HSMMtube	muscle
36	chr2:10586200-10589800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr2:10586400-10587400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr2:10586400-10587400	Enhancers	Colon Smooth Muscle	Colon
39	chr2:10586400-10587600	Flanking Active TSS	Duodenum Mucosa	Duodenum
40	chr2:10586400-10587600	Flanking Active TSS	Dnd41	blood
41	chr2:10586400-10587800	Flanking Active TSS	Fetal Muscle Leg	muscle
42	chr2:10586400-10588800	Active TSS	Colonic Mucosa	Colon
43	chr2:10586400-10589000	Active TSS	Hela-S3	cervix
44	chr2:10586600-10587400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr2:10586600-10587400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
46	chr2:10586600-10587400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
47	chr2:10586600-10587400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
48	chr2:10586600-10587400	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr2:10586600-10587400	Enhancers	Rectal Smooth Muscle	rectum
50	chr2:10586600-10587400	Flanking Active TSS	HepG2	liver

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