Variant report

Variant	rs9784670
Chromosome Location	chr5:177660239-177660240
allele	A/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	MXI1	chr5:177658286-177660241	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr5:177658603-177660497	GM12878	blood:	n/a	n/a
3	POLR2A	chr5:177660157-177660250	MCF-7	breast:	n/a	n/a
4	ELF1	chr5:177658701-177660260	MCF-7	breast:	n/a	n/a
5	POLR2A	chr5:177658872-177660281	GM18951	blood:	n/a	n/a
6	POLR2A	chr5:177658800-177660334	MCF10A-Er-Src	breast:	n/a	n/a
7	MAX	chr5:177658204-177660356	HepG2	liver:	n/a	chr5:177658594-177658604 chr5:177658621-177658631
8	POLR2A	chr5:177658156-177660670	GM18505	blood:	n/a	n/a
9	SMARCB1	chr5:177658048-177660271	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr5:177656552-177660493	HepG2	liver:	n/a	n/a
11	POLR2A	chr5:177659016-177660290	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr5:177658948-177660359	GM19193	blood:	n/a	n/a
13	POLR2A	chr5:177658083-177660606	K562	blood:	n/a	n/a
14	POLR2A	chr5:177657949-177660401	K562	blood:	n/a	n/a
15	POLR2A	chr5:177658770-177660246	GM12892	blood:	n/a	n/a
16	POLR2A	chr5:177658957-177660403	IMR90	lung:	n/a	n/a
17	BHLHE40	chr5:177658902-177660468	K562	blood:	n/a	chr5:177659901-177659917
18	HCFC1	chr5:177658696-177660329	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr5:177659293-177660301	GM12892	blood:	n/a	n/a
20	RCOR1	chr5:177659170-177660466	K562	blood:	n/a	n/a
21	STAT3	chr5:177659581-177660299	MCF10A-Er-Src	breast:	n/a	chr5:177659864-177659884 chr5:177659870-177659879 chr5:177659868-177659879 chr5:177659869-177659878 chr5:177659864-177659884 chr5:177659870-177659878
22	MXI1	chr5:177657403-177660266	SK-N-SH	brain:	n/a	n/a
23	JUN	chr5:177657564-177660508	K562	blood:	n/a	chr5:177658623-177658632
24	BACH1	chr5:177660141-177660312	K562	blood:	n/a	n/a
25	POLR2A	chr5:177658777-177660322	GM12878	blood:	n/a	n/a
26	SMARCC1	chr5:177658076-177660275	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr5:177659009-177660264	HUVEC	blood vessel:	n/a	n/a
28	STAT1	chr5:177659555-177660322	K562	blood:	n/a	chr5:177659864-177659884 chr5:177659870-177659879 chr5:177659869-177659878 chr5:177659864-177659884 chr5:177659868-177659879 chr5:177659870-177659878
29	ZBTB7A	chr5:177658903-177660293	ECC-1	luminal epithelium:	n/a	n/a
30	POLR2A	chr5:177658001-177660350	HL-60	blood:	n/a	n/a
31	RELA	chr5:177658657-177660259	GM15510	blood:	n/a	n/a
32	POLR2A	chr5:177658896-177660664	GM12878	blood:	n/a	n/a
33	POLR2A	chr5:177657897-177660434	HL-60	blood:	n/a	n/a
34	POLR2A	chr5:177657839-177660301	SK-N-MC	brain:	n/a	n/a
35	MAX	chr5:177658004-177660294	Hela-S3	cervix:	n/a	chr5:177658594-177658604 chr5:177658621-177658631
36	POLR2A	chr5:177658498-177660655	GM19099	blood:	n/a	n/a
37	POLR2A	chr5:177658802-177660484	MCF10A-Er-Src	breast:	n/a	n/a
38	MAFK	chr5:177659663-177660408	K562	blood:	n/a	n/a
39	MAZ	chr5:177658918-177660343	K562	blood:	n/a	n/a
40	POLR2A	chr5:177659050-177660316	GM12878	blood:	n/a	n/a
41	MAZ	chr5:177659091-177660600	GM12878	blood:	n/a	n/a
42	JUND	chr5:177660225-177660346	K562	blood:	n/a	n/a
43	STAT3	chr5:177659508-177660270	MCF10A-Er-Src	breast:	n/a	chr5:177659864-177659884 chr5:177659870-177659879 chr5:177659868-177659879 chr5:177659869-177659878 chr5:177659864-177659884 chr5:177659870-177659878
44	ELF1	chr5:177658324-177660369	GM12878	blood:	n/a	n/a
45	STAT1	chr5:177659106-177660483	Hela-S3	cervix:	n/a	chr5:177659864-177659884 chr5:177659870-177659879 chr5:177659869-177659878 chr5:177659864-177659884 chr5:177659868-177659879 chr5:177659870-177659878
46	CUX1	chr5:177659857-177660249	K562	blood:	n/a	n/a
47	CHD2	chr5:177659116-177660350	GM12878	blood:	n/a	n/a
48	MTA3	chr5:177659404-177660447	GM12878	blood:	n/a	n/a
49	POLR2A	chr5:177658760-177660739	Raji	blood:	n/a	n/a
50	POLR2A	chr5:177658848-177660304	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:177659087..177660769-chr5:178052015..178054177,2	K562	blood:
2	chr5:177659880..177662371-chr5:178030366..178033143,2	K562	blood:
3	chr5:177613072..177615957-chr5:177659065..177661764,2	MCF-7	breast:

Variant related genes	Relation type
PHYKPL	TF binding region
ENSG00000244234	Chromatin interaction
ENSG00000113240	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10036819	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10039093	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10061163	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10479615	1.00[CHB][hapmap]
rs13359656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13993	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1544925	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56077296	0.92[ASN][1000 genomes]
rs58593479	1.00[ASN][1000 genomes]
rs6872383	0.82[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs72819009	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs72819011	0.92[ASN][1000 genomes]
rs72819015	0.83[ASN][1000 genomes]
rs7715762	1.00[CEU][hapmap];0.82[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
3	nsv1019404	chr5:177507080-177859089	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	126 gene(s)	inside rSNPs	diseases
4	nsv482872	chr5:177580298-177744381	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	106 gene(s)	inside rSNPs	diseases
5	nsv1021981	chr5:177620372-177825272	Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	105 gene(s)	inside rSNPs	diseases
6	nsv537967	chr5:177620372-177825272	Active TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS 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	105 gene(s)	inside rSNPs	diseases
7	nsv1024689	chr5:177638936-177926244	Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv537968	chr5:177638936-177926244	Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv1018031	chr5:177655010-177746378	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
10	nsv537969	chr5:177655010-177746378	Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
11	nsv883195	chr5:177655194-177690539	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
12	nsv883196	chr5:177655194-177690978	Transcr. at gene 5' and 3' Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
13	nsv883197	chr5:177655194-177707204	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
14	nsv1025291	chr5:177657927-177756215	Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
15	nsv537970	chr5:177657927-177756215	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
16	esv3441517	chr5:177658571-177661119	Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
17	nsv527792	chr5:177659075-177675217	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
18	nsv883198	chr5:177659075-177690539	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177658400-177660400	Flanking Active TSS	Primary hematopoietic stem cells	blood
2	chr5:177658600-177660400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr5:177658600-177660400	Active TSS	Fetal Kidney	kidney
4	chr5:177658600-177660400	Flanking Active TSS	Stomach Smooth Muscle	stomach
5	chr5:177658800-177660400	Active TSS	HSMMtube	muscle
6	chr5:177659000-177660400	Active TSS	Primary T cells from cord blood	blood
7	chr5:177659000-177660400	Active TSS	Duodenum Mucosa	Duodenum
8	chr5:177659000-177660400	Active TSS	Fetal Lung	lung
9	chr5:177659200-177660400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr5:177659200-177660400	Enhancers	Fetal Brain Male	brain
11	chr5:177659400-177660400	Enhancers	Stomach Mucosa	stomach
12	chr5:177659600-177660400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr5:177659600-177660400	Flanking Active TSS	Adipose Nuclei	Adipose
14	chr5:177659800-177660400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr5:177659800-177660400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr5:177659800-177660400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr5:177659800-177660400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr5:177659800-177660400	Flanking Active TSS	Brain Germinal Matrix	brain
19	chr5:177659800-177660400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
20	chr5:177659800-177660400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
21	chr5:177659800-177660400	Enhancers	Spleen	Spleen
22	chr5:177659800-177660400	Flanking Active TSS	HepG2	liver
23	chr5:177659800-177660400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr5:177659800-177660600	Flanking Active TSS	Dnd41	blood
25	chr5:177659800-177665800	Weak transcription	Gastric	stomach
26	chr5:177660000-177660400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr5:177660000-177660400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
28	chr5:177660000-177660400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr5:177660000-177660400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
30	chr5:177660000-177660400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
31	chr5:177660000-177660400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr5:177660000-177660400	Flanking Active TSS	Brain Anterior Caudate	brain
33	chr5:177660000-177660400	Flanking Active TSS	Brain Cingulate Gyrus	brain
34	chr5:177660000-177660400	Flanking Active TSS	Brain Hippocampus Middle	brain
35	chr5:177660000-177660400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
36	chr5:177660000-177660400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr5:177660000-177660400	Flanking Active TSS	Brain Substantia Nigra	brain
38	chr5:177660000-177660400	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr5:177660000-177660400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
40	chr5:177660000-177660400	Flanking Active TSS	A549	lung
41	chr5:177660000-177660400	Flanking Active TSS	GM12878-XiMat	blood
42	chr5:177660000-177660400	Flanking Active TSS	Hela-S3	cervix
43	chr5:177660000-177660400	Flanking Active TSS	K562	blood
44	chr5:177660000-177660400	Flanking Active TSS	NHDF-Ad	bronchial
45	chr5:177660000-177660600	Enhancers	Placenta Amnion	Placenta Amnion
46	chr5:177660000-177661400	Weak transcription	HMEC	breast
47	chr5:177660000-177663400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr5:177660000-177663800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr5:177660000-177664600	Weak transcription	Small Intestine	intestine
50	chr5:177660200-177660400	Enhancers	H1 Cell Line	embryonic stem cell

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