Variant report

Variant	rs6942688
Chromosome Location	chr7:102575952-102575953
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	TCF12	chr7:102575782-102576547	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr7:102575865-102576456	SK-N-SH	brain:	n/a	n/a
3	TCF12	chr7:102575735-102576429	SK-N-SH	brain:	n/a	n/a
4	GATA3	chr7:102575852-102576220	SH-SY5Y	brain:	n/a	n/a
5	EP300	chr7:102575906-102576660	SK-N-SH_RA	brain:	n/a	n/a
6	RAD21	chr7:102575926-102576683	SK-N-SH_RA	brain:	n/a	n/a
7	POLR2A	chr7:102575911-102576353	SK-N-MC	brain:	n/a	n/a
8	GATA3	chr7:102575767-102576384	SK-N-SH	brain:	n/a	n/a
9	EP300	chr7:102573385-102577692	SK-N-SH	brain:	n/a	n/a
10	TEAD4	chr7:102575883-102576498	K562	blood:	n/a	n/a
11	CEBPB	chr7:102575862-102576164	K562	blood:	n/a	n/a
12	BHLHE40	chr7:102575929-102576160	K562	blood:	n/a	n/a
13	CEBPB	chr7:102575822-102576189	K562	blood:	n/a	n/a
14	CEBPB	chr7:102575871-102576286	K562	blood:	n/a	n/a
15	CCNT2	chr7:102575950-102576130	K562	blood:	n/a	n/a
16	CEBPD	chr7:102575905-102576325	K562	blood:	n/a	chr7:102575996-102576007
17	GATA2	chr7:102575909-102576259	SH-SY5Y	brain:	n/a	n/a
18	CEBPD	chr7:102575926-102576278	K562	blood:	n/a	chr7:102575996-102576007
19	ATF1	chr7:102575929-102576170	K562	blood:	n/a	n/a
20	RAD21	chr7:102575886-102576287	SK-N-SH_RA	brain:	n/a	n/a
21	GATA2	chr7:102575883-102576269	K562	blood:	n/a	n/a
22	POLR2A	chr7:102575940-102576291	SK-N-SH	brain:	n/a	n/a
23	RCOR1	chr7:102575845-102576264	K562	blood:	n/a	n/a
24	CEBPB	chr7:102575909-102576110	IMR90	lung:	n/a	n/a
25	EP300	chr7:102575837-102576491	SK-N-SH_RA	brain:	n/a	n/a

Variant related genes	Relation type
FBXL13	TF binding region
LRRC17	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12668311	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12670723	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12673840	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17136122	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28817087	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3800939	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4457269	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59099783	0.80[AMR][1000 genomes]
rs6465884	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6963884	0.90[EUR][1000 genomes]
rs6969209	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7798381	0.80[AMR][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
rs6942688	ZNF117	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:72 , 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	chr7:102573000-102576800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr7:102573000-102576800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr7:102573000-102577600	Genic enhancers	Fetal Stomach	stomach
8	chr7:102573200-102576200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr7:102573200-102577000	Enhancers	H9 Cell Line	embryonic stem cell
10	chr7:102573200-102578200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr7:102573400-102576800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr7:102573400-102578600	Weak transcription	Fetal Muscle Trunk	muscle
13	chr7:102573400-102579400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr7:102573400-102579800	Genic enhancers	Fetal Lung	lung
15	chr7:102573600-102577400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr7:102573800-102577200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
17	chr7:102573800-102591400	Weak transcription	Pancreas	Pancrea
18	chr7:102574000-102592200	Weak transcription	Fetal Intestine Large	intestine
19	chr7:102574200-102576800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr7:102574200-102579600	Weak transcription	Colon Smooth Muscle	Colon
21	chr7:102574400-102577600	Enhancers	Fetal Kidney	kidney
22	chr7:102574400-102578800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr7:102574600-102576400	Active TSS	Ovary	ovary
24	chr7:102574600-102576600	Weak transcription	Fetal Brain Male	brain
25	chr7:102574600-102577000	Active TSS	Right Atrium	heart
26	chr7:102574600-102577600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr7:102574600-102594400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr7:102574800-102576000	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr7:102574800-102576000	Genic enhancers	Fetal Muscle Leg	muscle
30	chr7:102574800-102576000	Weak transcription	K562	blood
31	chr7:102574800-102576600	Active TSS	Aorta	Aorta
32	chr7:102574800-102577600	Enhancers	H1 Cell Line	embryonic stem cell
33	chr7:102574800-102578400	Weak transcription	Fetal Brain Female	brain
34	chr7:102574800-102579800	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr7:102575000-102577400	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr7:102575000-102584400	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr7:102575000-102586000	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr7:102575000-102586800	Weak transcription	NHLF	lung
39	chr7:102575400-102576200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr7:102575400-102577000	Enhancers	Primary hematopoietic stem cells	blood
41	chr7:102575400-102577400	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr7:102575400-102577600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr7:102575400-102577600	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr7:102575400-102578600	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr7:102575400-102578800	Weak transcription	Small Intestine	intestine
46	chr7:102575400-102587000	Strong transcription	NH-A	brain
47	chr7:102575600-102576000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr7:102575600-102576200	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr7:102575600-102576400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr7:102575600-102576600	Weak transcription	Fetal Thymus	thymus

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