Variant report

Variant	rs73009861
Chromosome Location	chr1:147070456-147070457
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	MAZ	chr1:147070303-147073025	IMR90	lung:	n/a	chr1:147072841-147072851 chr1:147072253-147072263 chr1:147072658-147072667 chr1:147071284-147071294 chr1:147071315-147071325
2	SIN3A	chr1:147070386-147072756	H1-hESC	embryonic stem cell:	n/a	n/a
3	CHD1	chr1:147070383-147072260	IMR90	lung:	n/a	chr1:147071568-147071578 chr1:147071626-147071636 chr1:147071762-147071772 chr1:147071578-147071588 chr1:147071268-147071275
4	CTCF	chr1:147070380-147070530	WERI-Rb-1	eye:	n/a	n/a
5	POLR2A	chr1:147070399-147072282	H1-neurons	neurons:	n/a	n/a
6	JUND	chr1:147070243-147073063	SK-N-SH	brain:	n/a	chr1:147071760-147071769 chr1:147072658-147072668 chr1:147072659-147072667 chr1:147071280-147071289 chr1:147072657-147072668 chr1:147072706-147072717 chr1:147072659-147072667 chr1:147071571-147071580 chr1:147072658-147072668 chr1:147071393-147071402 chr1:147072709-147072719 chr1:147072660-147072667 chr1:147072710-147072718 chr1:147072658-147072668
7	GATA3	chr1:147070411-147070611	SH-SY5Y	brain:	n/a	n/a
8	HCFC1	chr1:147070439-147072985	Hela-S3	cervix:	n/a	n/a
9	GATA2	chr1:147070210-147071081	SH-SY5Y	brain:	n/a	n/a
10	CTCF	chr1:147070340-147070490	HCPEpiC	choroid plexus:	n/a	n/a
11	MXI1	chr1:147070300-147072473	IMR90	lung:	n/a	n/a
12	UBTF	chr1:147070437-147070482	K562	blood:	n/a	n/a
13	ELF1	chr1:147070292-147072217	MCF-7	breast:	n/a	chr1:147071754-147071766 chr1:147070999-147071011 chr1:147072164-147072176
14	POLR2A	chr1:147070447-147071788	SK-N-MC	brain:	n/a	n/a
15	POLR2A	chr1:147070410-147070500	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:146985951..146991555-chr1:147068919..147074935,7	MCF-7	breast:
2	chr1:147053305..147055800-chr1:147069628..147071755,2	K562	blood:
3	chr1:147070010..147071633-chr1:147096547..147098261,2	MCF-7	breast:
4	chr1:147050198..147052278-chr1:147069069..147071118,3	MCF-7	breast:
5	chr1:147012761..147015831-chr1:147068894..147072363,4	MCF-7	breast:
6	chr1:147008733..147014706-chr1:147069097..147075030,9	MCF-7	breast:

Variant related genes	Relation type
BCL9	TF binding region
ENSG00000116128	Chromatin interaction
ENSG00000234610	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12059427	1.00[EUR][1000 genomes]
rs12096043	1.00[AFR][1000 genomes]
rs12097989	1.00[AFR][1000 genomes]
rs57188402	0.86[AFR][1000 genomes]
rs59188898	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73007972	0.92[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872252	chr1:146471863-147398135	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	112 gene(s)	inside rSNPs	diseases
2	nsv999546	chr1:146507577-147356574	Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
3	nsv535123	chr1:146507577-147356574	Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
4	nsv492188	chr1:146507649-147381479	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
5	nsv916754	chr1:146507711-147417736	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	113 gene(s)	inside rSNPs	diseases
6	nsv547673	chr1:146510112-147398135	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
7	nsv547674	chr1:146522722-147396797	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	111 gene(s)	inside rSNPs	diseases
8	nsv998341	chr1:146531446-147384720	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
9	nsv535124	chr1:146531446-147384720	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
10	nsv1003493	chr1:146531446-147389944	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
11	nsv998209	chr1:146543722-147384720	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
12	nsv535126	chr1:146543722-147384720	Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	110 gene(s)	inside rSNPs	diseases
13	nsv872256	chr1:146556596-147410973	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
14	nsv1012331	chr1:146603479-147384720	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer 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	49 gene(s)	inside rSNPs	diseases
15	nsv535131	chr1:146603479-147384720	Genic enhancers Strong transcription Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
16	nsv1004849	chr1:146661516-147286826	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer 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	44 gene(s)	inside rSNPs	diseases
17	nsv535135	chr1:146661516-147286826	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
18	nsv534063	chr1:146807433-147381411	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
19	nsv831414	chr1:146884994-147083866	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
20	nsv1001868	chr1:146893791-147389944	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
21	nsv482606	chr1:146959127-147134517	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
22	nsv872266	chr1:147020099-147381558	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
23	esv3395068	chr1:147070353-147073501	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:147064200-147070600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:147069400-147070600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:147069800-147070600	Flanking Active TSS	Colon Smooth Muscle	Colon
4	chr1:147069800-147071200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr1:147070000-147070800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
6	chr1:147070000-147072400	Active TSS	Stomach Smooth Muscle	stomach
7	chr1:147070200-147070600	Flanking Bivalent TSS/Enh	H9 Cell Line	embryonic stem cell
8	chr1:147070200-147070600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
9	chr1:147070200-147070600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
10	chr1:147070200-147070600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
11	chr1:147070200-147070600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:147070200-147070600	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr1:147070200-147070600	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
14	chr1:147070200-147070600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr1:147070200-147070600	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:147070200-147070600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:147070200-147070600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:147070200-147070600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr1:147070200-147070600	Flanking Active TSS	Fetal Lung	lung
20	chr1:147070200-147070600	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
21	chr1:147070200-147070600	Bivalent/Poised TSS	Osteobl	bone
22	chr1:147070200-147070800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
23	chr1:147070200-147070800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:147070200-147070800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr1:147070200-147070800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
26	chr1:147070200-147070800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
27	chr1:147070200-147070800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr1:147070200-147070800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
29	chr1:147070200-147070800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
30	chr1:147070200-147070800	Flanking Active TSS	Fetal Brain Male	brain
31	chr1:147070200-147070800	Flanking Active TSS	Fetal Muscle Leg	muscle
32	chr1:147070200-147070800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
33	chr1:147070200-147071000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr1:147070200-147071000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
35	chr1:147070200-147071000	Flanking Active TSS	Fetal Brain Female	brain
36	chr1:147070200-147071200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
37	chr1:147070200-147071200	Flanking Active TSS	Liver	Liver
38	chr1:147070200-147071200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
39	chr1:147070200-147071400	Active TSS	Primary T cells from cord blood	blood
40	chr1:147070200-147072400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr1:147070200-147072400	Active TSS	Brain Angular Gyrus	brain
42	chr1:147070200-147072400	Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr1:147070200-147072400	Active TSS	Psoas Muscle	Psoas
44	chr1:147070200-147073000	Active TSS	Right Atrium	heart
45	chr1:147070200-147073200	Active TSS	Pancreatic Islets	Pancreatic Islet
46	chr1:147070200-147073600	Active TSS	ES-I3 Cell Line	embryonic stem cell
47	chr1:147070400-147070600	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr1:147070400-147070600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr1:147070400-147070600	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr1:147070400-147070600	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links