Variant report

Variant	rs12092798
Chromosome Location	chr1:160071819-160071820
allele	C/T
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:9)
LncRNA
region (count:0)
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	SMC3	chr1:160070515-160072207	SK-N-SH	brain:	n/a	chr1:160070945-160070959
2	POLR2A	chr1:160071735-160072170	H1-neurons	neurons:	n/a	n/a
3	RFX5	chr1:160070579-160072148	IMR90	lung:	n/a	chr1:160071881-160071894
4	CTCF	chr1:160071800-160071950	WERI-Rb-1	eye:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:160070092..160072124-chr1:160188156..160190319,2	MCF-7	breast:
2	chr1:160070906..160071899-chr1:160221233..160221914,2	MCF-7	breast:
3	chr1:160071459..160074798-chr1:160230293..160234240,4	K562	blood:
4	chr1:160071057..160072737-chr1:160310768..160312526,2	K562	blood:
5	chr1:160071153..160073617-chr1:160073631..160075783,2	MCF-7	breast:
6	chr1:160069814..160072169-chr1:160152055..160154283,2	K562	blood:
7	chr1:160068906..160070835-chr1:160071784..160074235,2	K562	blood:
8	chr1:160068738..160071829-chr1:160174520..160176851,4	MCF-7	breast:
9	chr1:160069126..160071871-chr1:160230770..160232513,2	MCF-7	breast:

No data

Variant related genes	Relation type
IGSF8	TF binding region
ENSG00000228606	Chromatin interaction
ENSG00000265381	Chromatin interaction
ENSG00000162734	Chromatin interaction
ENSG00000132716	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1131891	0.87[CEU][hapmap]
rs12401728	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12402888	0.87[CEU][hapmap]
rs12408242	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2295621	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2295622	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3747619	0.87[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3327316	chr1:159985477-160151281	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv520189	chr1:160011512-160095625	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Weak transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv1806746	chr1:160029416-160105927	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases
4	esv1824420	chr1:160029416-160105927	Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv1843994	chr1:160029416-160105927	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv534066	chr1:160029416-160105986	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	29 gene(s)	inside rSNPs	diseases
7	esv1794281	chr1:160029416-160111565	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	esv1820784	chr1:160029416-160159395	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
9	nsv534165	chr1:160029416-160187302	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12092798	ZBTB7B	cis	cerebellum	SCAN
rs12092798	SMG5	cis	parietal	SCAN
rs12092798	IGSF8	cis	cerebellum	SCAN
rs12092798	PEX19	cis	parietal	SCAN
rs12092798	LY9	cis	cerebellum	SCAN
rs12092798	CASQ1	cis	parietal	SCAN
rs12092798	KCNN3	cis	cerebellum	SCAN
rs12092798	IGSF8	cis	parietal	SCAN
rs12092798	CD1B	cis	parietal	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160069200-160074800	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr1:160069400-160072000	Enhancers	Primary T cells fromperipheralblood	blood
3	chr1:160069400-160072400	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr1:160069400-160072600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:160069400-160073000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:160069400-160073600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr1:160069400-160075600	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr1:160069400-160075600	Enhancers	Fetal Muscle Leg	muscle
9	chr1:160069600-160072400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr1:160070400-160074600	Enhancers	H1 Cell Line	embryonic stem cell
11	chr1:160070400-160074800	Enhancers	Fetal Muscle Trunk	muscle
12	chr1:160070400-160075000	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr1:160070600-160072200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:160070600-160072400	Enhancers	Stomach Mucosa	stomach
15	chr1:160070600-160072600	Enhancers	K562	blood
16	chr1:160070600-160074400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:160070600-160074400	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr1:160070600-160074400	Enhancers	Fetal Brain Male	brain
19	chr1:160070600-160074800	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr1:160070800-160072600	Enhancers	Fetal Heart	heart
21	chr1:160070800-160072800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr1:160071000-160072000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr1:160071000-160072000	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr1:160071000-160072000	Enhancers	Fetal Intestine Large	intestine
25	chr1:160071000-160072200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
26	chr1:160071000-160072400	Enhancers	Fetal Kidney	kidney
27	chr1:160071000-160072800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
28	chr1:160071000-160072800	Enhancers	Muscle Satellite Cultured Cells	--
29	chr1:160071000-160072800	Flanking Active TSS	Stomach Smooth Muscle	stomach
30	chr1:160071000-160073000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:160071000-160073000	Enhancers	Psoas Muscle	Psoas
32	chr1:160071000-160073000	Enhancers	Osteobl	bone
33	chr1:160071000-160073200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr1:160071000-160073200	Enhancers	Rectal Mucosa Donor 31	rectum
35	chr1:160071000-160073200	Enhancers	A549	lung
36	chr1:160071000-160073400	Enhancers	Fetal Intestine Small	intestine
37	chr1:160071000-160074400	Enhancers	Ovary	ovary
38	chr1:160071000-160074600	Enhancers	Brain Germinal Matrix	brain
39	chr1:160071000-160074600	Enhancers	HSMM	muscle
40	chr1:160071000-160074800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:160071000-160074800	Enhancers	Fetal Lung	lung
42	chr1:160071000-160074800	Enhancers	Fetal Stomach	stomach
43	chr1:160071000-160074800	Enhancers	HSMMtube	muscle
44	chr1:160071200-160073000	Enhancers	Right Ventricle	heart
45	chr1:160071200-160074800	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr1:160071200-160074800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr1:160071200-160077600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr1:160071400-160072000	Weak transcription	Aorta	Aorta
49	chr1:160071400-160072200	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr1:160071400-160072200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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