Variant report

Variant	rs55815241
Chromosome Location	chr9:1050114-1050115
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	TCF7L2	chr9:1049925-1050789	MCF-7	breast:	n/a	n/a
2	SETDB1	chr9:1049973-1050403	U2OS	brain:	n/a	n/a
3	CTCF	chr9:1050060-1050210	HEEpiC	esophagus:	n/a	n/a
4	ELF1	chr9:1049892-1050803	MCF-7	breast:	n/a	n/a
5	MAX	chr9:1049855-1050705	MCF-7	breast:	n/a	chr9:1050415-1050425
6	ELF1	chr9:1049820-1050778	MCF-7	breast:	n/a	n/a
7	CTCF	chr9:1050060-1050210	SAEC	small airway:	n/a	n/a
8	NR2F2	chr9:1049559-1051045	MCF-7	breast:	n/a	n/a
9	SIN3AK20	chr9:1049585-1050984	MCF-7	breast:	n/a	n/a
10	EGR1	chr9:1049954-1050743	MCF-7	breast:	n/a	chr9:1050415-1050428 chr9:1050416-1050427 chr9:1050415-1050428 chr9:1050411-1050433 chr9:1050415-1050428 chr9:1050418-1050427 chr9:1050418-1050428
11	MAX	chr9:1049940-1050692	ECC-1	luminal epithelium:	n/a	chr9:1050415-1050425
12	MAX	chr9:1050049-1050686	ECC-1	luminal epithelium:	n/a	chr9:1050415-1050425
13	CTCF	chr9:1050060-1050210	NHEK	skin:	n/a	n/a
14	MAX	chr9:1049882-1050623	A549	lung:	n/a	chr9:1050415-1050425
15	NFYB	chr9:1050053-1050517	GM12878	blood:	n/a	chr9:1050275-1050287 chr9:1050245-1050259 chr9:1050276-1050291 chr9:1050244-1050256 chr9:1050245-1050260 chr9:1050276-1050291 chr9:1050245-1050260 chr9:1050276-1050289 chr9:1050276-1050290
16	RAD21	chr9:1049622-1050740	MCF-7	breast:	n/a	n/a
17	CTCF	chr9:1050060-1050210	HMF	breast:	n/a	n/a
18	ZNF217	chr9:1049668-1050775	MCF-7	breast:	n/a	n/a
19	CHD2	chr9:1050113-1050403	H1-hESC	embryonic stem cell:	n/a	n/a
20	CTCF	chr9:1050020-1050170	Caco-2	colon:	n/a	n/a
21	CTCF	chr9:1050080-1050230	HCPEpiC	choroid plexus:	n/a	n/a
22	NFIC	chr9:1049957-1050534	ECC-1	luminal epithelium:	n/a	n/a
23	GATA3	chr9:1049788-1050947	MCF-7	breast:	n/a	n/a
24	SP1	chr9:1050096-1050356	H1-hESC	embryonic stem cell:	n/a	chr9:1050216-1050227 chr9:1050213-1050227 chr9:1050277-1050298
25	MAX	chr9:1049597-1051056	MCF-7	breast:	n/a	chr9:1050415-1050425
26	POLR2A	chr9:1050080-1050684	MCF-7	breast:	n/a	n/a
27	E2F6	chr9:1050082-1050633	H1-hESC	embryonic stem cell:	n/a	chr9:1050435-1050442 chr9:1050247-1050256 chr9:1050278-1050287 chr9:1050418-1050428 chr9:1050435-1050442 chr9:1050435-1050442 chr9:1050434-1050446
28	E2F6	chr9:1050007-1050728	H1-hESC	embryonic stem cell:	n/a	chr9:1050435-1050442 chr9:1050247-1050256 chr9:1050278-1050287 chr9:1050418-1050428 chr9:1050435-1050442 chr9:1050435-1050442 chr9:1050434-1050446
29	RFX5	chr9:1049994-1050310	HepG2	liver:	n/a	chr9:1050265-1050280 chr9:1050279-1050288 chr9:1050248-1050257
30	E2F4	chr9:1050031-1050563	MCF10A-Er-Src	breast:	n/a	chr9:1050435-1050442 chr9:1050247-1050256 chr9:1050278-1050287 chr9:1050418-1050428 chr9:1050435-1050442 chr9:1050435-1050442 chr9:1050434-1050446
31	HA-E2F1	chr9:1049789-1051165	MCF-7	breast:	n/a	chr9:1050435-1050442 chr9:1050247-1050256 chr9:1050278-1050287 chr9:1050418-1050428 chr9:1050435-1050442 chr9:1050435-1050442 chr9:1050434-1050446
32	HDAC2	chr9:1049873-1050813	MCF-7	breast:	n/a	chr9:1050512-1050531
33	HDAC2	chr9:1049621-1050809	MCF-7	breast:	n/a	chr9:1050512-1050531
34	EGR1	chr9:1050008-1050822	MCF-7	breast:	n/a	chr9:1050415-1050428 chr9:1050416-1050427 chr9:1050415-1050428 chr9:1050411-1050433 chr9:1050415-1050428 chr9:1050418-1050427 chr9:1050418-1050428
35	NR2F2	chr9:1049956-1050800	MCF-7	breast:	n/a	n/a
36	CHD2	chr9:1050104-1050417	GM12878	blood:	n/a	n/a
37	NFYB	chr9:1050095-1050451	K562	blood:	n/a	chr9:1050275-1050287 chr9:1050245-1050259 chr9:1050276-1050291 chr9:1050244-1050256 chr9:1050245-1050260 chr9:1050276-1050291 chr9:1050245-1050260 chr9:1050276-1050289 chr9:1050276-1050290
38	POLR2A	chr9:1049803-1053615	SK-N-MC	brain:	n/a	n/a

Variant related genes	Relation type
DMRT2	TF binding region

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

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10121975	1.00[EUR][1000 genomes]
rs16927146	1.00[EUR][1000 genomes]
rs16928356	1.00[EUR][1000 genomes]
rs35541630	1.00[EUR][1000 genomes]
rs57487518	1.00[EUR][1000 genomes]
rs57558840	1.00[EUR][1000 genomes]
rs59155009	1.00[EUR][1000 genomes]
rs60301829	1.00[EUR][1000 genomes]
rs7041977	1.00[EUR][1000 genomes]
rs73380471	1.00[EUR][1000 genomes]
rs73380482	1.00[EUR][1000 genomes]
rs73380483	1.00[EUR][1000 genomes]
rs73382412	1.00[EUR][1000 genomes]
rs73382420	1.00[EUR][1000 genomes]
rs73382438	1.00[EUR][1000 genomes]
rs73382440	1.00[EUR][1000 genomes]
rs73386518	1.00[EUR][1000 genomes]
rs73386558	1.00[EUR][1000 genomes]
rs7390001	1.00[EUR][1000 genomes]
rs7859422	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025492	chr9:478813-1157169	Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv539897	chr9:478813-1157169	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS 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 miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv613037	chr9:643453-1138368	Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv817248	chr9:706283-1457665	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv892010	chr9:841152-1069663	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1034070	chr9:911265-1152351	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1016222	chr9:999390-1284180	Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv1025752	chr9:1003311-1124524	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1027466	chr9:1007196-1097053	Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1033117	chr9:1007196-1129306	Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv1016321	chr9:1034594-1592366	Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv539908	chr9:1034594-1592366	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:1048200-1051000	Enhancers	Gastric	stomach
2	chr9:1048400-1051400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
3	chr9:1048600-1050400	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
4	chr9:1049400-1050200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
5	chr9:1049600-1050200	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
6	chr9:1049600-1050200	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
7	chr9:1049600-1050400	Bivalent Enhancer	Fetal Stomach	stomach
8	chr9:1049600-1050800	Flanking Active TSS	Adipose Nuclei	Adipose
9	chr9:1049600-1051600	Enhancers	Pancreas	Pancrea
10	chr9:1049600-1053400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
11	chr9:1049800-1050200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr9:1049800-1050200	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
13	chr9:1049800-1050200	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr9:1049800-1050200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr9:1049800-1050200	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
16	chr9:1049800-1050200	Active TSS	Right Ventricle	heart
17	chr9:1049800-1050200	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
18	chr9:1049800-1050200	Bivalent Enhancer	HepG2	liver
19	chr9:1049800-1050400	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr9:1049800-1050400	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr9:1049800-1050400	Bivalent/Poised TSS	Brain Angular Gyrus	brain
22	chr9:1049800-1050400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
23	chr9:1049800-1050400	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
24	chr9:1049800-1050600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
25	chr9:1049800-1050600	Bivalent/Poised TSS	Primary T cells from cord blood	blood
26	chr9:1049800-1050600	Bivalent Enhancer	Stomach Mucosa	stomach
27	chr9:1049800-1050600	Bivalent/Poised TSS	A549	lung
28	chr9:1049800-1050800	Flanking Bivalent TSS/Enh	Brain Anterior Caudate	brain
29	chr9:1049800-1050800	Bivalent Enhancer	Fetal Heart	heart
30	chr9:1049800-1050800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
31	chr9:1049800-1051000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
32	chr9:1049800-1051600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
33	chr9:1049800-1052200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
34	chr9:1049800-1052200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
35	chr9:1049800-1053000	Active TSS	Psoas Muscle	Psoas
36	chr9:1049800-1053200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
37	chr9:1049800-1053200	Bivalent Enhancer	Liver	Liver
38	chr9:1050000-1050200	Bivalent/Poised TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr9:1050000-1050200	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
40	chr9:1050000-1050200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr9:1050000-1050200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr9:1050000-1050200	Flanking Bivalent TSS/Enh	Fetal Kidney	kidney
43	chr9:1050000-1050200	Flanking Bivalent TSS/Enh	Fetal Lung	lung
44	chr9:1050000-1050200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
45	chr9:1050000-1050200	Bivalent Enhancer	NHEK	skin
46	chr9:1050000-1050400	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr9:1050000-1050400	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
48	chr9:1050000-1050400	Bivalent/Poised TSS	Brain Germinal Matrix	brain
49	chr9:1050000-1050400	Active TSS	Colonic Mucosa	Colon
50	chr9:1050000-1050400	Bivalent/Poised TSS	Fetal Brain Female	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links