Variant report

Variant	rs56136178
Chromosome Location	chr1:78449605-78449606
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr1:78448984-78449657	A549	lung:	n/a	n/a
2	FOXA2	chr1:78449095-78449611	A549	lung:	n/a	n/a
3	POLR2A	chr1:78449476-78449892	HepG2	liver:	n/a	n/a
4	FOXA1	chr1:78449187-78449955	HepG2	liver:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:78447431..78449969-chr1:78468449..78471656,4	MCF-7	breast:
2	chr1:78449418..78451643-chr1:78468794..78470733,2	MCF-7	breast:
3	chr1:78447842..78450094-chr1:78543814..78546165,2	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DNAJB4-1	chr1:78444779-78456066	NONHSAT004062

No data

Variant related genes	Relation type
FUBP1	TF binding region
ENSG00000162616	Chromatin interaction
ENSG00000273338	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1007335	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12027636	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41309165	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56236539	0.92[EUR][1000 genomes]
rs56708272	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56728070	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs57314531	0.92[EUR][1000 genomes]
rs57604233	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60470980	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6689438	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71244405	0.92[EUR][1000 genomes]
rs74090701	0.83[EUR][1000 genomes]
rs74092308	0.92[EUR][1000 genomes]
rs74092324	0.92[EUR][1000 genomes]
rs74092339	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74092341	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74092348	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9663066	0.92[EUR][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	esv1794082	chr1:78102426-78492221	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	esv3434340	chr1:78153780-78607103	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv518855	chr1:78416669-78456355	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78445800-78449800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:78446000-78449800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr1:78446000-78449800	Weak transcription	Small Intestine	intestine
4	chr1:78446000-78451800	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr1:78446000-78452600	Weak transcription	Gastric	stomach
6	chr1:78446000-78455600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:78446000-78458600	Weak transcription	Fetal Muscle Trunk	muscle
8	chr1:78446000-78458800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:78446000-78461000	Weak transcription	Placenta	Placenta
10	chr1:78446200-78451800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr1:78446200-78452400	Weak transcription	Psoas Muscle	Psoas
12	chr1:78446200-78452600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:78446200-78457200	Weak transcription	Fetal Muscle Leg	muscle
14	chr1:78446200-78461200	Weak transcription	Fetal Stomach	stomach
15	chr1:78446200-78469600	Weak transcription	Thymus	Thymus
16	chr1:78446400-78451800	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr1:78446400-78458200	Weak transcription	Fetal Thymus	thymus
18	chr1:78446400-78469800	Weak transcription	Primary B cells from peripheral blood	blood
19	chr1:78446400-78470200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr1:78446600-78449800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr1:78446600-78450000	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr1:78446600-78450000	Weak transcription	Fetal Heart	heart
23	chr1:78446600-78450600	Weak transcription	HSMMtube	muscle
24	chr1:78446600-78450800	Weak transcription	Primary B cells from cord blood	blood
25	chr1:78446600-78450800	Enhancers	HepG2	liver
26	chr1:78446600-78451800	Weak transcription	Right Atrium	heart
27	chr1:78446600-78457200	Weak transcription	Primary T cells from cord blood	blood
28	chr1:78446600-78459200	Weak transcription	Fetal Brain Female	brain
29	chr1:78446600-78460800	Weak transcription	Stomach Smooth Muscle	stomach
30	chr1:78446600-78461200	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr1:78446600-78468000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr1:78446600-78468400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:78446600-78468800	Weak transcription	Primary hematopoietic stem cells	blood
34	chr1:78446600-78468800	Weak transcription	Adipose Nuclei	Adipose
35	chr1:78446600-78468800	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr1:78446600-78469000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr1:78446600-78469000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr1:78446600-78469000	Weak transcription	Fetal Kidney	kidney
39	chr1:78446600-78469600	Weak transcription	Aorta	Aorta
40	chr1:78446600-78469800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr1:78446600-78470200	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr1:78446600-78470400	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr1:78446800-78449800	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr1:78446800-78450200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:78446800-78450800	Weak transcription	Colon Smooth Muscle	Colon
46	chr1:78446800-78452000	Weak transcription	HMEC	breast
47	chr1:78446800-78452400	Weak transcription	NHEK	skin
48	chr1:78446800-78452600	Weak transcription	NHLF	lung
49	chr1:78446800-78452800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:78446800-78454200	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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