Variant report

Variant	rs55681588
Chromosome Location	chr7:102577338-102577339
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	EP300	chr7:102573385-102577692	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:102574165..102576650-chr7:102576864..102579530,2	K562	blood:
2	chr7:102574165..102576596-chr7:102576864..102579639,2	K562	blood:

Variant related genes	Relation type
FBXL13	TF binding region
ENSG00000161040	Chromatin interaction
ENSG00000128606	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10487281	1.00[ASN][1000 genomes]
rs10487284	1.00[ASN][1000 genomes]
rs11496066	1.00[ASN][1000 genomes]
rs12113073	1.00[ASN][1000 genomes]
rs17135875	1.00[ASN][1000 genomes]
rs17135913	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17135916	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17474893	1.00[ASN][1000 genomes]
rs2041094	1.00[ASN][1000 genomes]
rs2228687	0.89[EUR][1000 genomes]
rs2411061	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3893651	1.00[ASN][1000 genomes]
rs4377880	1.00[ASN][1000 genomes]
rs4398822	1.00[ASN][1000 genomes]
rs55781834	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55849741	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55851590	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56314487	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56336567	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56692051	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6465886	0.86[EUR][1000 genomes]
rs66712128	0.89[EUR][1000 genomes]
rs6955064	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6964296	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6968036	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs727175	1.00[ASN][1000 genomes]
rs73192015	1.00[ASN][1000 genomes]
rs73192019	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73192025	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73192026	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73714541	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7779854	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7781557	1.00[ASN][1000 genomes]
rs7798582	0.89[EUR][1000 genomes]
rs7809047	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016563	chr7:101912320-102695860	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1028438	chr7:101912320-102704135	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv868996	chr7:102332827-102991361	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	esv2752138	chr7:102358320-102787135	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv464667	chr7:102486254-102624192	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv608060	chr7:102486254-102624192	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55681588	LRRC17	cis	Stomach	GTEx

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102517200-102578200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr7:102571400-102579600	Genic enhancers	HSMM	muscle
3	chr7:102571600-102581800	Weak transcription	Fetal Intestine Small	intestine
4	chr7:102571800-102579400	Weak transcription	Left Ventricle	heart
5	chr7:102573000-102577600	Genic enhancers	Fetal Stomach	stomach
6	chr7:102573200-102578200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr7:102573400-102578600	Weak transcription	Fetal Muscle Trunk	muscle
8	chr7:102573400-102579400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr7:102573400-102579800	Genic enhancers	Fetal Lung	lung
10	chr7:102573600-102577400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr7:102573800-102591400	Weak transcription	Pancreas	Pancrea
12	chr7:102574000-102592200	Weak transcription	Fetal Intestine Large	intestine
13	chr7:102574200-102579600	Weak transcription	Colon Smooth Muscle	Colon
14	chr7:102574400-102577600	Enhancers	Fetal Kidney	kidney
15	chr7:102574400-102578800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr7:102574600-102577600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr7:102574600-102594400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr7:102574800-102577600	Enhancers	H1 Cell Line	embryonic stem cell
19	chr7:102574800-102578400	Weak transcription	Fetal Brain Female	brain
20	chr7:102574800-102579800	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr7:102575000-102577400	Enhancers	iPS-15b Cell Line	embryonic stem cell
22	chr7:102575000-102584400	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr7:102575000-102586000	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr7:102575000-102586800	Weak transcription	NHLF	lung
25	chr7:102575400-102577400	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr7:102575400-102577600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr7:102575400-102577600	Enhancers	Monocytes-CD14+_RO01746	blood
28	chr7:102575400-102578600	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr7:102575400-102578800	Weak transcription	Small Intestine	intestine
30	chr7:102575400-102587000	Strong transcription	NH-A	brain
31	chr7:102575600-102577400	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr7:102575600-102577400	Enhancers	Primary hematopoietic stem cells short term culture	blood
33	chr7:102575600-102577600	Enhancers	HUES48 Cell Line	embryonic stem cell
34	chr7:102575600-102578400	Weak transcription	HUVEC	blood vessel
35	chr7:102575600-102578800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr7:102575600-102578800	Weak transcription	Liver	Liver
37	chr7:102575600-102579000	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr7:102575600-102579400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr7:102575600-102581600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr7:102575600-102583000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr7:102575600-102585200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr7:102575600-102586800	Weak transcription	Osteobl	bone
43	chr7:102576000-102579800	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr7:102576800-102577400	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr7:102576800-102577400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr7:102576800-102578200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr7:102576800-102578400	Weak transcription	Adipose Nuclei	Adipose
48	chr7:102576800-102579400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr7:102576800-102582000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr7:102576800-102582400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links