Variant report

Variant	rs3845392
Chromosome Location	chr1:180122985-180122986
allele	C/T
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	POLR2A	chr1:180122889-180123878	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr1:180122966-180123901	HL-60	blood:	n/a	n/a
3	POLR2A	chr1:180122896-180124310	PBDE	blood:	n/a	n/a
4	POLR2A	chr1:180122678-180124264	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr1:180122604-180124286	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr1:180122827-180124275	NB4	blood:	n/a	n/a
7	POLR2A	chr1:180122547-180123875	PANC-1	pancreas:	n/a	n/a
8	CHD1	chr1:180122641-180127045	IMR90	lung:	n/a	chr1:180124562-180124572
9	POLR2A	chr1:180122937-180124249	GM12891	blood:	n/a	n/a
10	POLR2A	chr1:180122896-180124361	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr1:180122713-180124263	MCF10A-Er-Src	breast:	n/a	n/a
12	POLR2A	chr1:180122841-180125159	IMR90	lung:	n/a	n/a
13	POLR2A	chr1:180122580-180124215	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr1:180122719-180124730	HUVEC	blood vessel:	n/a	n/a
15	POLR2A	chr1:180122043-180124190	K562	blood:	n/a	n/a
16	POLR2A	chr1:180122767-180124259	GM12878	blood:	n/a	n/a
17	MXI1	chr1:180122822-180125322	SK-N-SH	brain:	n/a	chr1:180123364-180123379 chr1:180123945-180123954 chr1:180124358-180124367
18	MTA3	chr1:180122978-180123871	GM12878	blood:	n/a	n/a
19	POLR2A	chr1:180122884-180124244	SK-N-MC	brain:	n/a	n/a
20	MXI1	chr1:180122494-180128394	IMR90	lung:	n/a	chr1:180123364-180123379 chr1:180123945-180123954 chr1:180124358-180124367
21	POLR2A	chr1:180122848-180124301	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:179844379..179846987-chr1:180122185..180123975,2	MCF-7	breast:
2	chr1:179844894..179847778-chr1:180122782..180124340,2	K562	blood:
3	chr1:180060321..180062626-chr1:180121553..180123534,4	MCF-7	breast:
4	chr1:179849468..179853023-chr1:180122560..180126275,4	K562	blood:
5	chr1:179843719..179847778-chr1:180121939..180127812,8	K562	blood:
6	chr1:180122502..180123389-chr11:62608695..62609423,2	HCT-116	colon:
7	chr1:180122867..180124515-chr12:122237701..122240027,2	MCF-7	breast:
8	chr1:179923898..179926923-chr1:180121889..180124249,4	MCF-7	breast:
9	chr1:180109932..180112525-chr1:180121644..180123894,2	MCF-7	breast:

Variant related genes	Relation type
QSOX1	TF binding region
ENSG00000169905	Chromatin interaction
ENSG00000212694	Chromatin interaction
ENSG00000272906	Chromatin interaction
ENSG00000143337	Chromatin interaction
ENSG00000135837	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000139725	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs35481032	0.93[ASN][1000 genomes]
rs3753812	0.92[ASN][1000 genomes]
rs3767193	0.91[ASN][1000 genomes]
rs3767196	0.92[ASN][1000 genomes]
rs3820311	0.92[ASN][1000 genomes]
rs3820312	0.93[ASN][1000 genomes]
rs7531169	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv1003739	chr1:180027760-180483292	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv535217	chr1:180027760-180483292	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv1012558	chr1:180027960-180217613	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers 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
5	nsv535218	chr1:180027960-180217613	Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv497930	chr1:180031321-180220723	Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv533073	chr1:180031328-180217612	Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer 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
8	nsv916937	chr1:180031328-180220685	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS 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
9	nsv1007590	chr1:180121480-180236452	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
10	nsv999104	chr1:180121480-180242659	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
11	esv3355160	chr1:180122754-180125702	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180118400-180123000	Weak transcription	Right Atrium	heart
2	chr1:180119600-180123000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr1:180119600-180123000	Enhancers	NHDF-Ad	bronchial
4	chr1:180119600-180123000	Enhancers	NHLF	lung
5	chr1:180120400-180123000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:180121000-180123000	Weak transcription	Primary B cells from cord blood	blood
7	chr1:180121200-180123000	Weak transcription	HSMMtube	muscle
8	chr1:180121400-180123000	Weak transcription	Placenta	Placenta
9	chr1:180121400-180123000	Weak transcription	HSMM	muscle
10	chr1:180121400-180123000	Enhancers	HUVEC	blood vessel
11	chr1:180121400-180123000	Weak transcription	NH-A	brain
12	chr1:180122000-180123000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr1:180122200-180123000	Weak transcription	HMEC	breast
14	chr1:180122400-180123000	Enhancers	Pancreas	Pancrea
15	chr1:180122400-180123200	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:180122400-180124600	Active TSS	Esophagus	oesophagus
17	chr1:180122400-180125000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr1:180122600-180123000	Bivalent Enhancer	HepG2	liver
19	chr1:180122800-180123000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:180122800-180123000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
21	chr1:180122800-180123000	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
22	chr1:180122800-180123000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr1:180122800-180123000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:180122800-180123000	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr1:180122800-180123000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:180122800-180123000	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr1:180122800-180123000	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr1:180122800-180123000	Enhancers	Primary B cells from peripheral blood	blood
29	chr1:180122800-180123000	Enhancers	Primary T cells from cord blood	blood
30	chr1:180122800-180123000	Enhancers	Primary hematopoietic stem cells	blood
31	chr1:180122800-180123000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr1:180122800-180123000	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr1:180122800-180123000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr1:180122800-180123000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr1:180122800-180123000	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr1:180122800-180123000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr1:180122800-180123000	Enhancers	Primary T helper cells fromperipheralblood	blood
38	chr1:180122800-180123000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr1:180122800-180123000	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr1:180122800-180123000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:180122800-180123000	Enhancers	Muscle Satellite Cultured Cells	--
42	chr1:180122800-180123000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr1:180122800-180123000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr1:180122800-180123000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr1:180122800-180123000	Enhancers	Brain Angular Gyrus	brain
46	chr1:180122800-180123000	Enhancers	Brain Anterior Caudate	brain
47	chr1:180122800-180123000	Enhancers	Brain Cingulate Gyrus	brain
48	chr1:180122800-180123000	Active TSS	Brain Hippocampus Middle	brain
49	chr1:180122800-180123000	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr1:180122800-180123000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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