Variant report

Variant	rs11715496
Chromosome Location	chr3:48633245-48633246
allele	A/C
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	SP1	chr3:48632497-48633743	A549	lung:	n/a	chr3:48632846-48632855 chr3:48633063-48633072 chr3:48633063-48633073 chr3:48632773-48632782 chr3:48633062-48633074 chr3:48633435-48633447 chr3:48633063-48633073 chr3:48633062-48633074 chr3:48632769-48632783 chr3:48632844-48632856 chr3:48633059-48633073 chr3:48632844-48632856 chr3:48632845-48632855 chr3:48632840-48632854 chr3:48632772-48632784 chr3:48632845-48632859 chr3:48633435-48633447 chr3:48632772-48632784 chr3:48632774-48632783 chr3:48633064-48633073
2	POLR2A	chr3:48631344-48633991	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr3:48631746-48635203	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr3:48632471-48634476	U87	brain:	n/a	n/a
5	CEBPB	chr3:48633214-48633534	A549	lung:	n/a	n/a
6	RCOR1	chr3:48632878-48633293	K562	blood:	n/a	n/a
7	NR3C1	chr3:48632742-48633534	A549	lung:	n/a	n/a
8	POLR2A	chr3:48633186-48635705	GM12878	blood:	n/a	n/a
9	ZNF143	chr3:48632486-48633487	Hela-S3	cervix:	n/a	chr3:48633055-48633073
10	FOS	chr3:48632898-48633433	MCF10A-Er-Src	breast:	n/a	chr3:48633085-48633092 chr3:48633085-48633094 chr3:48633083-48633095 chr3:48633083-48633094 chr3:48633084-48633093 chr3:48633084-48633094
11	ELF1	chr3:48633087-48633431	K562	blood:	n/a	n/a
12	SIN3AK20	chr3:48632898-48633455	SK-N-SH	brain:	n/a	n/a
13	FOSL2	chr3:48632851-48633396	SK-N-SH	brain:	n/a	chr3:48633085-48633092 chr3:48633085-48633094 chr3:48633083-48633095 chr3:48633084-48633093 chr3:48633084-48633094
14	TCF12	chr3:48632709-48633796	SK-N-SH	brain:	n/a	n/a
15	PBX3	chr3:48632835-48633579	SK-N-SH	brain:	n/a	n/a
16	JUND	chr3:48632957-48633416	MCF-7	breast:	n/a	chr3:48633085-48633092 chr3:48633085-48633094 chr3:48633083-48633095 chr3:48633084-48633093 chr3:48633084-48633094 chr3:48633083-48633094
17	POLR2A	chr3:48632952-48636594	SK-N-MC	brain:	n/a	n/a
18	MYC	chr3:48632993-48633317	K562	blood:	n/a	n/a
19	MAZ	chr3:48632431-48633925	IMR90	lung:	n/a	chr3:48633412-48633422 chr3:48632836-48632846
20	RFX5	chr3:48632742-48633527	Hela-S3	cervix:	n/a	n/a
21	MAZ	chr3:48632909-48633466	K562	blood:	n/a	chr3:48633412-48633422
22	POLR2A	chr3:48630527-48636597	U87	brain:	n/a	n/a
23	NR3C1	chr3:48632844-48633579	A549	lung:	n/a	n/a
24	FOSL2	chr3:48632859-48633293	MCF-7	breast:	n/a	chr3:48633085-48633092 chr3:48633085-48633094 chr3:48633083-48633095 chr3:48633084-48633093 chr3:48633084-48633094
25	CEBPB	chr3:48632610-48633580	Hela-S3	cervix:	n/a	n/a
26	EP300	chr3:48632850-48633573	Hela-S3	cervix:	n/a	chr3:48633334-48633341 chr3:48633085-48633094
27	FOXA2	chr3:48632810-48633587	A549	lung:	n/a	n/a
28	POLR2A	chr3:48632981-48633318	HCT-116	colon:	n/a	n/a
29	BCL3	chr3:48632541-48633833	A549	lung:	n/a	chr3:48632723-48632736 chr3:48632774-48632783 chr3:48632719-48632728 chr3:48632713-48632726 chr3:48632722-48632731 chr3:48632911-48632920 chr3:48632716-48632729
30	TCF7L2	chr3:48632918-48633467	Hela-S3	cervix:	n/a	chr3:48633085-48633094 chr3:48633084-48633093
31	POLR2A	chr3:48633190-48633927	H1-neurons	neurons:	n/a	n/a
32	ATF3	chr3:48632846-48633268	K562	blood:	n/a	n/a
33	FOSL2	chr3:48632714-48633721	SK-N-SH	brain:	n/a	chr3:48633085-48633092 chr3:48632833-48632842 chr3:48633085-48633094 chr3:48633083-48633095 chr3:48633084-48633093 chr3:48633084-48633094 chr3:48632834-48632843
34	JUND	chr3:48632468-48633752	A549	lung:	n/a	chr3:48633085-48633092 chr3:48632833-48632842 chr3:48633085-48633094 chr3:48633083-48633095 chr3:48633084-48633093 chr3:48633084-48633094 chr3:48632834-48632843 chr3:48633083-48633094
35	FOXA2	chr3:48632985-48633655	A549	lung:	n/a	n/a
36	GATA3	chr3:48632478-48633969	A549	lung:	n/a	chr3:48633886-48633896
37	RAD21	chr3:48632846-48633520	Hela-S3	cervix:	n/a	n/a
38	CCNT2	chr3:48632998-48633261	K562	blood:	n/a	chr3:48633063-48633072
39	POLR2A	chr3:48632996-48633302	HCT-116	colon:	n/a	n/a
40	POLR2A	chr3:48631649-48633648	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr3:48632463-48634567	H1-hESC	embryonic stem cell:	n/a	n/a
42	FOSL2	chr3:48632856-48634072	HepG2	liver:	n/a	chr3:48633085-48633092 chr3:48633085-48633094 chr3:48633083-48633095 chr3:48633084-48633093 chr3:48633084-48633094
43	NR3C1	chr3:48632885-48633606	A549	lung:	n/a	n/a
44	GTF2F1	chr3:48632910-48633777	Hela-S3	cervix:	n/a	n/a
45	FOSL1	chr3:48632854-48633308	K562	blood:	n/a	chr3:48633085-48633092 chr3:48633085-48633094 chr3:48633083-48633095 chr3:48633084-48633093 chr3:48633083-48633094 chr3:48633084-48633094
46	MAZ	chr3:48631898-48633929	Hela-S3	cervix:	n/a	chr3:48632417-48632427 chr3:48633412-48633422 chr3:48632836-48632846
47	BHLHE40	chr3:48633034-48633439	K562	blood:	n/a	n/a
48	MAX	chr3:48631588-48634054	A549	lung:	n/a	chr3:48632417-48632427 chr3:48633412-48633422 chr3:48632836-48632846
49	NFIC	chr3:48632754-48633689	SK-N-SH	brain:	n/a	chr3:48633268-48633284 chr3:48633268-48633285
50	REST	chr3:48632468-48633757	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:48504584..48507240-chr3:48631582..48633525,2	MCF-7	breast:
2	chr3:48631354..48634791-chr3:48635080..48639274,6	MCF-7	breast:
3	chr3:48631939..48633856-chr3:48671693..48673580,2	K562	blood:
4	chr3:48633231..48638086-chr3:48639417..48644972,8	MCF-7	breast:
5	chr3:48631986..48633856-chr3:48672080..48674450,2	K562	blood:
6	chr3:48633143..48634875-chr3:48635486..48637467,3	MCF-7	breast:
7	chr3:48632939..48635012-chr3:48667249..48669292,2	MCF-7	breast:

Variant related genes	Relation type
COL7A1	TF binding region
ENSG00000010256	Chromatin interaction
ENSG00000213689	Chromatin interaction
ENSG00000225697	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11706087	1.00[EUR][1000 genomes]
rs11706153	1.00[AMR][1000 genomes]
rs11707229	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs11712752	1.00[AMR][1000 genomes]
rs11919537	1.00[LWK][hapmap]
rs1352421	1.00[LWK][hapmap]
rs2229820	1.00[MKK][hapmap]
rs6414612	1.00[ASN][1000 genomes]
rs6442128	0.86[EUR][1000 genomes]
rs6807104	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008232	chr3:48517121-48702416	Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv523981	chr3:48520289-48721040	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1004383	chr3:48543794-48649772	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv876762	chr3:48591481-48731487	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv3811	chr3:48599180-48643809	Enhancers Genic enhancers Flanking Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	nsv818138	chr3:48610925-48731487	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
8	nsv590246	chr3:48628014-48721040	Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48620000-48634600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:48620000-48634600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr3:48631600-48633400	Bivalent Enhancer	Stomach Mucosa	stomach
4	chr3:48631800-48633400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
5	chr3:48631800-48633800	Enhancers	Gastric	stomach
6	chr3:48631800-48636000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr3:48631800-48637000	Enhancers	Fetal Heart	heart
8	chr3:48632000-48633400	Flanking Active TSS	Osteobl	bone
9	chr3:48632000-48633800	Enhancers	HSMMtube	muscle
10	chr3:48632400-48633400	Bivalent Enhancer	Fetal Brain Male	brain
11	chr3:48632400-48635200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr3:48632400-48635200	Weak transcription	Brain Substantia Nigra	brain
13	chr3:48632400-48638600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:48632600-48633400	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
15	chr3:48632600-48633600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr3:48632600-48633600	Enhancers	Pancreas	Pancrea
17	chr3:48632600-48633600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
18	chr3:48632600-48634400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:48632600-48635000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr3:48632600-48635000	Weak transcription	Aorta	Aorta
21	chr3:48632600-48635600	Enhancers	NHDF-Ad	bronchial
22	chr3:48632600-48636000	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr3:48632600-48636400	Weak transcription	Brain Angular Gyrus	brain
24	chr3:48632600-48639000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr3:48632800-48633400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
26	chr3:48632800-48633400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr3:48632800-48633400	Enhancers	Colon Smooth Muscle	Colon
28	chr3:48632800-48633400	Bivalent Enhancer	Duodenum Smooth Muscle	Duodenum
29	chr3:48632800-48633400	Enhancers	Fetal Intestine Small	intestine
30	chr3:48632800-48633400	Enhancers	Rectal Mucosa Donor 29	rectum
31	chr3:48632800-48633400	Enhancers	Rectal Smooth Muscle	rectum
32	chr3:48632800-48633400	Enhancers	HUVEC	blood vessel
33	chr3:48632800-48633600	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr3:48632800-48633600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr3:48632800-48633600	Bivalent Enhancer	Colonic Mucosa	Colon
36	chr3:48632800-48633600	Bivalent Enhancer	Fetal Muscle Leg	muscle
37	chr3:48632800-48633600	Bivalent Enhancer	Fetal Stomach	stomach
38	chr3:48632800-48633800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr3:48632800-48633800	Bivalent Enhancer	Brain Germinal Matrix	brain
40	chr3:48632800-48633800	Enhancers	Duodenum Mucosa	Duodenum
41	chr3:48632800-48633800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
42	chr3:48632800-48633800	Bivalent Enhancer	Fetal Lung	lung
43	chr3:48632800-48634000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr3:48632800-48634200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr3:48632800-48634200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr3:48632800-48634400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
47	chr3:48632800-48634600	Enhancers	Right Ventricle	heart
48	chr3:48632800-48634800	Enhancers	Placenta	Placenta
49	chr3:48632800-48635000	Weak transcription	Brain Hippocampus Middle	brain
50	chr3:48632800-48635000	Enhancers	Left Ventricle	heart

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