Variant report

Variant	rs56239346
Chromosome Location	chr2:38979467-38979468
allele	A/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	chr2:38979320-38979626	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr2:38973281-38979491	K562	blood:	n/a	n/a
3	MYC	chr2:38977326-38979642	K562	blood:	n/a	chr2:38977600-38977609 chr2:38979316-38979323 chr2:38978721-38978731 chr2:38979315-38979326 chr2:38978724-38978734
4	MXI1	chr2:38979214-38979475	K562	blood:	n/a	n/a
5	POLR2A	chr2:38977062-38979559	K562	blood:	n/a	n/a
6	MAX	chr2:38977162-38979575	HepG2	liver:	n/a	chr2:38977600-38977609 chr2:38979316-38979323 chr2:38978721-38978731 chr2:38979315-38979326 chr2:38978724-38978734
7	HCFC1	chr2:38977335-38979602	Hela-S3	cervix:	n/a	n/a
8	HEY1	chr2:38977277-38979542	HepG2	liver:	n/a	n/a
9	MYC	chr2:38977785-38979473	H1-hESC	embryonic stem cell:	n/a	chr2:38979316-38979323 chr2:38978721-38978731 chr2:38979315-38979326 chr2:38978724-38978734
10	REST	chr2:38977226-38979675	H1-neurons	neurons:	n/a	chr2:38977794-38977804 chr2:38978974-38978983 chr2:38978212-38978222 chr2:38978584-38978592 chr2:38979114-38979134
11	POLR2A	chr2:38976768-38979496	PANC-1	pancreas:	n/a	n/a
12	MYC	chr2:38977429-38979480	K562	blood:	n/a	chr2:38977600-38977609 chr2:38979316-38979323 chr2:38978721-38978731 chr2:38979315-38979326 chr2:38978724-38978734
13	MAX	chr2:38977122-38979583	A549	lung:	n/a	chr2:38977600-38977609 chr2:38979316-38979323 chr2:38978721-38978731 chr2:38979315-38979326 chr2:38978724-38978734
14	POLR2A	chr2:38977038-38979481	HepG2	liver:	n/a	n/a
15	POLR2A	chr2:38976575-38979505	SK-N-MC	brain:	n/a	n/a
16	MXI1	chr2:38973236-38979955	SK-N-SH	brain:	n/a	chr2:38978665-38978680
17	TBP	chr2:38976970-38979495	K562	blood:	n/a	n/a
18	MYC	chr2:38977168-38979549	K562	blood:	n/a	chr2:38977600-38977609 chr2:38979316-38979323 chr2:38978721-38978731 chr2:38979315-38979326 chr2:38978724-38978734
19	TCF12	chr2:38976855-38979513	A549	lung:	n/a	n/a
20	POLR2A	chr2:38967761-38979649	H1-hESC	embryonic stem cell:	n/a	n/a
21	NR2F2	chr2:38978089-38979468	K562	blood:	n/a	n/a
22	MYC	chr2:38977372-38979490	K562	blood:	n/a	chr2:38977600-38977609 chr2:38979316-38979323 chr2:38978721-38978731 chr2:38979315-38979326 chr2:38978724-38978734
23	MYC	chr2:38976566-38979508	A549	lung:	n/a	chr2:38977600-38977609 chr2:38979316-38979323 chr2:38978721-38978731 chr2:38979315-38979326 chr2:38978724-38978734
24	TEAD4	chr2:38977758-38979600	HepG2	liver:	n/a	n/a
25	NFYA	chr2:38979466-38979635	GM12878	blood:	n/a	n/a
26	MXI1	chr2:38976601-38979588	IMR90	lung:	n/a	chr2:38978665-38978680
27	TEAD4	chr2:38977084-38979556	K562	blood:	n/a	n/a
28	MAX	chr2:38977023-38979618	A549	lung:	n/a	chr2:38977600-38977609 chr2:38979316-38979323 chr2:38978721-38978731 chr2:38979315-38979326 chr2:38978724-38978734
29	MXI1	chr2:38977261-38979467	HepG2	liver:	n/a	chr2:38978665-38978680
30	MAX	chr2:38979171-38979471	K562	blood:	n/a	chr2:38979316-38979323 chr2:38979315-38979326
31	MAX	chr2:38977275-38979559	HepG2	liver:	n/a	chr2:38977600-38977609 chr2:38979316-38979323 chr2:38978721-38978731 chr2:38979315-38979326 chr2:38978724-38978734
32	MAX	chr2:38977797-38979532	H1-hESC	embryonic stem cell:	n/a	chr2:38979316-38979323 chr2:38978721-38978731 chr2:38979315-38979326 chr2:38978724-38978734

No.	Distal block	Cell Line	Cell type
1	chr2:38977870..38980067-chr2:42586942..42589703,3	K562	blood:
2	chr2:38819128..38833161-chr2:38974716..38980003,37	K562	blood:
3	chr2:38976936..38979845-chr2:39101241..39105632,7	K562	blood:
4	chr2:38976938..38979508-chr2:39454441..39457000,2	K562	blood:
5	chr2:38816358..38820230-chr2:38976960..38979820,4	MCF-7	breast:
6	chr2:38760428..38762981-chr2:38976976..38979591,3	K562	blood:
7	chr2:38976877..38979785-chr2:39100480..39105632,13	K562	blood:
8	chr2:38976218..38980921-chr2:39003670..39007764,15	K562	blood:
9	chr2:37457826..37459742-chr2:38976926..38979723,2	K562	blood:
10	chr2:38816516..38836019-chr2:38963690..38980163,62	K562	blood:
11	chr2:38762042..38765801-chr2:38976684..38979922,4	MCF-7	breast:
12	chr2:38824074..38831950-chr2:38975822..38980618,12	MCF-7	breast:
13	chr2:38978307..38979883-chr20:23342389..23345213,2	MCF-7	breast:
14	chr2:38828577..38831705-chr2:38976861..38979916,6	MCF-7	breast:
15	chr2:38891861..38895889-chr2:38976029..38979857,7	K562	blood:
16	chr2:38975148..38982473-chr2:39000165..39007764,21	K562	blood:
17	chr2:38879772..38882593-chr2:38978947..38981476,2	K562	blood:
18	chr2:38974221..38979921-chr2:38986851..38994572,21	K562	blood:
19	chr2:38602255..38605343-chr2:38976114..38979530,4	K562	blood:
20	chr2:38974982..38979904-chr2:39002191..39014206,31	MCF-7	breast:
21	chr2:38977122..38981176-chr2:38994666..38999219,6	K562	blood:
22	chr2:38977033..38979904-chr2:47402717..47404547,2	K562	blood:
23	chr2:38892007..38895113-chr2:38976994..38979857,4	K562	blood:
24	chr12:7012428..7015040-chr2:38976959..38979555,2	K562	blood:
25	chr2:38975156..38979928-chr2:39002986..39007194,11	MCF-7	breast:
26	chr2:38824770..38827325-chr2:38977013..38980268,3	MCF-7	breast:
27	chr2:38976319..38979796-chr2:38988969..38996616,16	MCF-7	breast:
28	chr2:38977048..38979806-chr2:39045778..39047764,3	MCF-7	breast:
29	chr2:38977749..38979717-chr2:39155350..39158126,2	K562	blood:
30	chr2:38973912..38980240-chr2:38989822..38999883,17	MCF-7	breast:

Variant related genes	Relation type
SRSF7	TF binding region
ENSG00000152147	Chromatin interaction
ENSG00000010626	Chromatin interaction
ENSG00000232114	Chromatin interaction
ENSG00000188010	Chromatin interaction
ENSG00000115944	Chromatin interaction
ENSG00000214694	Chromatin interaction
ENSG00000205111	Chromatin interaction
ENSG00000119787	Chromatin interaction
ENSG00000143891	Chromatin interaction
ENSG00000125812	Chromatin interaction
ENSG00000115816	Chromatin interaction
ENSG00000163214	Chromatin interaction
ENSG00000235586	Chromatin interaction
ENSG00000227238	Chromatin interaction
ENSG00000143889	Chromatin interaction
ENSG00000003509	Chromatin interaction
ENSG00000143933	Chromatin interaction
ENSG00000271443	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11888905	1.00[AMR][1000 genomes]
rs11892292	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11894209	1.00[AMR][1000 genomes]
rs11899756	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4592827	1.00[AMR][1000 genomes]
rs55809581	1.00[AMR][1000 genomes]
rs56407729	1.00[AMR][1000 genomes]
rs58080550	1.00[AMR][1000 genomes]
rs58449189	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59364009	1.00[AMR][1000 genomes]
rs60895887	1.00[AMR][1000 genomes]
rs61139307	1.00[AMR][1000 genomes]
rs61556896	1.00[AMR][1000 genomes]
rs6708518	1.00[AMR][1000 genomes]
rs6724203	1.00[AMR][1000 genomes]
rs6756998	1.00[AMR][1000 genomes]
rs73930361	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73930365	1.00[AMR][1000 genomes]
rs73930366	1.00[AMR][1000 genomes]
rs73930371	1.00[AMR][1000 genomes]
rs73930376	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	esv1798055	chr2:38955865-39039504	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38976800-38979600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr2:38977200-38979600	Active TSS	H1 Cell Line	embryonic stem cell
3	chr2:38978600-38979600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
4	chr2:38978800-38979600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
5	chr2:38978800-38979600	Flanking Active TSS	Dnd41	blood
6	chr2:38978800-38979800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
7	chr2:38979000-38981400	Weak transcription	Ovary	ovary
8	chr2:38979200-38979600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr2:38979200-38979600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
10	chr2:38979200-38979600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr2:38979200-38979600	Enhancers	Primary B cells from peripheral blood	blood
12	chr2:38979200-38979600	Enhancers	Primary T cells from cord blood	blood
13	chr2:38979200-38979600	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr2:38979200-38979600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr2:38979200-38979600	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr2:38979200-38979600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr2:38979200-38979600	Flanking Active TSS	A549	lung
18	chr2:38979200-38979600	Flanking Active TSS	K562	blood
19	chr2:38979200-38979600	Enhancers	NHEK	skin
20	chr2:38979200-38979800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr2:38979200-38979800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr2:38979200-38979800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
23	chr2:38979200-38979800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr2:38979200-38979800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr2:38979200-38979800	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr2:38979200-38979800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr2:38979200-38979800	Enhancers	Pancreatic Islets	Pancreatic Islet
28	chr2:38979200-38979800	Enhancers	Fetal Lung	lung
29	chr2:38979200-38979800	Flanking Active TSS	HepG2	liver
30	chr2:38979200-38980800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr2:38979200-38981400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr2:38979200-38981400	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr2:38979200-38981400	Weak transcription	Right Atrium	heart
34	chr2:38979200-38983800	Weak transcription	HSMM	muscle
35	chr2:38979200-39005000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr2:38979400-38979600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr2:38979400-38979600	Enhancers	Primary T cells fromperipheralblood	blood
38	chr2:38979400-38979600	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr2:38979400-38979600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr2:38979400-38979600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr2:38979400-38979600	Active TSS	Brain Germinal Matrix	brain
42	chr2:38979400-38979600	Enhancers	Fetal Intestine Small	intestine
43	chr2:38979400-38979600	Enhancers	Hela-S3	cervix
44	chr2:38979400-38979600	Enhancers	NH-A	brain
45	chr2:38979400-38979800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:38979400-38979800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr2:38979400-38979800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr2:38979400-38979800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr2:38979400-38979800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
50	chr2:38979400-38979800	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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