Variant report

Variant	rs56339196
Chromosome Location	chr2:55458662-55458663
allele	C/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	MTA3	chr2:55458589-55461547	GM12878	blood:	n/a	n/a
2	HCFC1	chr2:55458624-55460325	K562	blood:	n/a	n/a
3	ELF1	chr2:55458502-55460607	HCT-116	colon:	n/a	chr2:55459306-55459319
4	SRF	chr2:55458647-55459625	ECC-1	luminal epithelium:	n/a	chr2:55458909-55458923 chr2:55458905-55458919 chr2:55458907-55458920 chr2:55458907-55458920 chr2:55458908-55458925 chr2:55458909-55458918 chr2:55458903-55458921 chr2:55458906-55458921 chr2:55458907-55458918 chr2:55458905-55458923 chr2:55458905-55458922
5	MAX	chr2:55458583-55460929	A549	lung:	n/a	n/a
6	POLR2A	chr2:55458589-55462559	HCT-116	colon:	n/a	n/a
7	POLR2A	chr2:55458627-55465420	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr2:55458643-55463921	SK-N-MC	brain:	n/a	n/a
9	SRF	chr2:55458454-55460313	HCT-116	colon:	n/a	chr2:55458909-55458923 chr2:55458905-55458919 chr2:55458907-55458920 chr2:55458907-55458920 chr2:55458908-55458925 chr2:55458909-55458918 chr2:55458903-55458921 chr2:55458906-55458921 chr2:55458907-55458918 chr2:55458905-55458923 chr2:55458905-55458922
10	ELF1	chr2:55458560-55460252	MCF-7	breast:	n/a	chr2:55459306-55459319
11	ELK1	chr2:55458622-55460326	K562	blood:	n/a	chr2:55459307-55459316 chr2:55459307-55459316
12	ELF1	chr2:55458636-55459961	A549	lung:	n/a	chr2:55459306-55459319
13	ELF1	chr2:55458616-55460290	HCT-116	colon:	n/a	chr2:55459306-55459319
14	MYBL2	chr2:55458596-55460585	HepG2	liver:	n/a	n/a
15	EP300	chr2:55458585-55459960	K562	blood:	n/a	chr2:55458752-55458766 chr2:55459308-55459315
16	TAF1	chr2:55458653-55460646	A549	lung:	n/a	n/a
17	REST	chr2:55458597-55460470	A549	lung:	n/a	n/a
18	ELF1	chr2:55458631-55460117	MCF-7	breast:	n/a	chr2:55459306-55459319
19	ELK1	chr2:55458652-55459966	Hela-S3	cervix:	n/a	chr2:55459307-55459316 chr2:55459307-55459316
20	MXI1	chr2:55458504-55461434	SK-N-SH	brain:	n/a	n/a
21	ELF1	chr2:55458653-55460013	K562	blood:	n/a	chr2:55459306-55459319
22	ELF1	chr2:55458660-55460012	HepG2	liver:	n/a	chr2:55459306-55459319
23	GABPA	chr2:55458383-55460250	MCF-7	breast:	n/a	chr2:55459343-55459350
24	SRF	chr2:55458478-55460591	HCT-116	colon:	n/a	chr2:55458909-55458923 chr2:55458905-55458919 chr2:55458907-55458920 chr2:55458907-55458920 chr2:55458908-55458925 chr2:55458909-55458918 chr2:55458903-55458921 chr2:55458906-55458921 chr2:55458907-55458918 chr2:55458905-55458923 chr2:55458905-55458922
25	ELF1	chr2:55458643-55460057	HepG2	liver:	n/a	chr2:55459306-55459319
26	GABPA	chr2:55458451-55460089	A549	lung:	n/a	chr2:55459343-55459350
27	GABPA	chr2:55458630-55460179	SK-N-SH	brain:	n/a	chr2:55459343-55459350
28	MXI1	chr2:55458649-55460708	IMR90	lung:	n/a	n/a
29	ELK4	chr2:55458601-55459942	Hela-S3	cervix:	n/a	chr2:55459307-55459316 chr2:55459305-55459316
30	GATA2	chr2:55458652-55460015	SH-SY5Y	brain:	n/a	chr2:55458675-55458685 chr2:55458677-55458684 chr2:55458670-55458691 chr2:55458675-55458684
31	SRF	chr2:55458572-55460039	ECC-1	luminal epithelium:	n/a	chr2:55458909-55458923 chr2:55458905-55458919 chr2:55458907-55458920 chr2:55458907-55458920 chr2:55458908-55458925 chr2:55458909-55458918 chr2:55458903-55458921 chr2:55458906-55458921 chr2:55458907-55458918 chr2:55458905-55458923 chr2:55458905-55458922
32	GABPA	chr2:55458586-55460145	MCF-7	breast:	n/a	chr2:55459343-55459350
33	SRF	chr2:55458528-55460156	MCF-7	breast:	n/a	chr2:55458909-55458923 chr2:55458905-55458919 chr2:55458907-55458920 chr2:55458907-55458920 chr2:55458908-55458925 chr2:55458909-55458918 chr2:55458903-55458921 chr2:55458906-55458921 chr2:55458907-55458918 chr2:55458905-55458923 chr2:55458905-55458922
34	GATA1	chr2:55458660-55460783	PBDE	blood:	n/a	chr2:55458675-55458685 chr2:55458677-55458684 chr2:55458670-55458691 chr2:55458675-55458684
35	GABPA	chr2:55458647-55460016	SK-N-SH	brain:	n/a	chr2:55459343-55459350
36	HCFC1	chr2:55458485-55461515	Hela-S3	cervix:	n/a	n/a
37	IRF1	chr2:55458621-55460594	K562	blood:	n/a	chr2:55458947-55458961
38	GABPA	chr2:55458604-55460206	A549	lung:	n/a	chr2:55459343-55459350
39	POLR2A	chr2:55458451-55467274	MCF10A-Er-Src	breast:	n/a	n/a
40	E2F6	chr2:55458575-55460046	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:55458112..55461105-chr2:55507986..55510921,3	MCF-7	breast:
2	chr2:54195792..54198215-chr2:55457941..55460893,2	K562	blood:
3	chr2:55275304..55279887-chr2:55458370..55461390,5	K562	blood:
4	chr2:55458256..55462359-chr2:55494864..55497801,3	K562	blood:
5	chr2:55276121..55279274-chr2:55457448..55460901,6	K562	blood:
6	chr2:55458256..55461079-chr2:55494634..55496499,3	K562	blood:
7	chr2:55458277..55462347-chr2:55843080..55846218,4	K562	blood:
8	chr2:55458156..55461118-chr2:55494163..55499368,6	MCF-7	breast:
9	chr2:55457538..55465596-chr2:55493335..55497971,13	MCF-7	breast:

Variant related genes	Relation type
RPS27A	TF binding region
ENSG00000162997	Chromatin interaction
ENSG00000085760	Chromatin interaction
ENSG00000068878	Chromatin interaction
ENSG00000272606	Chromatin interaction
ENSG00000170634	Chromatin interaction
ENSG00000115310	Chromatin interaction
ENSG00000138041	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1133181	0.82[ASN][1000 genomes]
rs1133182	0.82[ASN][1000 genomes]
rs11679663	0.82[ASN][1000 genomes]
rs12616435	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12619400	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12621144	0.82[ASN][1000 genomes]
rs13012766	0.82[ASN][1000 genomes]
rs13019355	0.82[ASN][1000 genomes]
rs13021215	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13023235	0.80[ASN][1000 genomes]
rs14026	0.82[ASN][1000 genomes]
rs2164714	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2576710	0.87[ASN][1000 genomes]
rs2576724	0.96[ASN][1000 genomes]
rs2864818	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs34054131	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35026006	0.84[ASN][1000 genomes]
rs35161040	0.87[ASN][1000 genomes]
rs35890669	0.83[ASN][1000 genomes]
rs3762509	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3935223	0.81[ASN][1000 genomes]
rs4420737	0.83[ASN][1000 genomes]
rs4671241	0.82[ASN][1000 genomes]
rs4671242	0.82[ASN][1000 genomes]
rs4672026	0.81[ASN][1000 genomes]
rs56095114	0.85[ASN][1000 genomes]
rs6545478	0.82[ASN][1000 genomes]
rs6758504	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7595134	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522016	chr2:55404794-55560298	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3348896	chr2:55429540-55498552	Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56339196	FLJ31438	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55451000-55458800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:55451000-55458800	Weak transcription	Esophagus	oesophagus
3	chr2:55451000-55458800	Weak transcription	Stomach Mucosa	stomach
4	chr2:55451400-55458800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr2:55453000-55458800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:55455800-55458800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr2:55456000-55458800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr2:55456200-55459000	Weak transcription	Spleen	Spleen
9	chr2:55456600-55458800	Weak transcription	Gastric	stomach
10	chr2:55457000-55459000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:55457600-55458800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr2:55457600-55458800	Flanking Active TSS	Dnd41	blood
13	chr2:55457800-55460000	Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr2:55457800-55460400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr2:55457800-55460400	Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr2:55458000-55458800	Enhancers	Primary T cells fromperipheralblood	blood
17	chr2:55458000-55458800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr2:55458000-55460200	Active TSS	A549	lung
19	chr2:55458000-55460400	Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr2:55458200-55460000	Active TSS	K562	blood
21	chr2:55458200-55460200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr2:55458200-55460400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr2:55458200-55460600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr2:55458200-55460800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr2:55458200-55460800	Active TSS	HMEC	breast
26	chr2:55458400-55458800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr2:55458400-55458800	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr2:55458400-55458800	Enhancers	Primary B cells from peripheral blood	blood
29	chr2:55458400-55458800	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr2:55458400-55458800	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr2:55458400-55458800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr2:55458400-55458800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr2:55458400-55458800	Flanking Active TSS	Brain Anterior Caudate	brain
34	chr2:55458400-55458800	Flanking Active TSS	Brain Germinal Matrix	brain
35	chr2:55458400-55458800	Flanking Active TSS	Fetal Lung	lung
36	chr2:55458400-55458800	Flanking Active TSS	HepG2	liver
37	chr2:55458400-55458800	Flanking Active TSS	NHDF-Ad	bronchial
38	chr2:55458400-55458800	Flanking Active TSS	Osteobl	bone
39	chr2:55458400-55459000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
40	chr2:55458400-55459000	Flanking Active TSS	Brain Angular Gyrus	brain
41	chr2:55458400-55459000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
42	chr2:55458400-55459000	Flanking Active TSS	Duodenum Mucosa	Duodenum
43	chr2:55458400-55459000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
44	chr2:55458400-55459000	Flanking Active TSS	HUVEC	blood vessel
45	chr2:55458400-55459200	Flanking Active TSS	Primary hematopoietic stem cells	blood
46	chr2:55458400-55459200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr2:55458400-55459200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
48	chr2:55458400-55459400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr2:55458400-55459400	Flanking Active TSS	Liver	Liver
50	chr2:55458400-55459800	Active TSS	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links