Variant report

Variant	rs7248439
Chromosome Location	chr19:42925577-42925578
allele	A/G
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	GATA3	chr19:42925357-42926281	MCF-7	breast:	n/a	chr19:42925616-42925623 chr19:42926032-42926042 chr19:42925616-42925623 chr19:42925615-42925623 chr19:42925616-42925623 chr19:42925612-42925628
2	GATA3	chr19:42925478-42925749	T-47D	breast:	n/a	chr19:42925616-42925623 chr19:42925616-42925623 chr19:42925615-42925623 chr19:42925616-42925623 chr19:42925612-42925628
3	GATA3	chr19:42925423-42926184	MCF-7	breast:	n/a	chr19:42925616-42925623 chr19:42926032-42926042 chr19:42925616-42925623 chr19:42925615-42925623 chr19:42925616-42925623 chr19:42925612-42925628

No.	Distal block	Cell Line	Cell type
1	chr19:42787574..42789864-chr19:42923760..42926145,2	MCF-7	breast:
2	chr19:42637501..42639898-chr19:42924232..42925782,2	K562	blood:
3	chr19:42925339..42926995-chr19:42928878..42931861,2	K562	blood:
4	chr19:42924851..42926943-chr19:42928310..42931390,3	MCF-7	breast:
5	chr19:42903448..42905839-chr19:42923535..42926055,2	MCF-7	breast:

Variant related genes	Relation type
LIPE-AS1	TF binding region
ENSG00000268605	Chromatin interaction
ENSG00000079432	Chromatin interaction
ENSG00000266226	Chromatin interaction
ENSG00000213904	Chromatin interaction
ENSG00000079435	Chromatin interaction
ENSG00000254887	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10405152	0.81[AMR][1000 genomes]
rs10405891	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10411253	1.00[EUR][1000 genomes]
rs10414969	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10416062	1.00[EUR][1000 genomes]
rs10416915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10417560	0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10418997	0.81[AMR][1000 genomes]
rs10422000	1.00[EUR][1000 genomes]
rs10422191	0.81[AMR][1000 genomes]
rs10422283	0.80[AFR][1000 genomes]
rs10423047	1.00[EUR][1000 genomes]
rs10423136	1.00[EUR][1000 genomes]
rs10425139	1.00[EUR][1000 genomes]
rs11882701	0.81[AMR][1000 genomes]
rs13343840	0.81[AMR][1000 genomes]
rs13345659	0.95[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16975743	0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16975750	0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16975799	0.81[AMR][1000 genomes]
rs16975862	0.81[AMR][1000 genomes]
rs17340417	0.92[AMR][1000 genomes]
rs28448880	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28514561	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28625452	0.81[AMR][1000 genomes]
rs35623577	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7245385	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7251638	1.00[EUR][1000 genomes]
rs7252470	1.00[EUR][1000 genomes]
rs7254369	0.92[AMR][1000 genomes]
rs7254839	1.00[EUR][1000 genomes]
rs7255015	1.00[EUR][1000 genomes]
rs73556352	1.00[EUR][1000 genomes]
rs73556356	1.00[EUR][1000 genomes]
rs8102976	1.00[EUR][1000 genomes]
rs8103108	1.00[EUR][1000 genomes]
rs8104731	0.81[AMR][1000 genomes]
rs9917002	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv911782	chr19:42514712-42931004	Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	nsv526186	chr19:42676481-43203507	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
5	esv2422471	chr19:42733141-43669485	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
6	nsv911788	chr19:42887492-42930652	Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
7	nsv911792	chr19:42901430-42929254	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv911793	chr19:42901430-42929502	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers 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	15 gene(s)	inside rSNPs	diseases
9	nsv911794	chr19:42901430-42930652	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv911795	chr19:42901430-42932699	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription 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	15 gene(s)	inside rSNPs	diseases
11	nsv911798	chr19:42904653-42930652	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv911799	chr19:42905645-42930652	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
13	nsv911800	chr19:42906914-42930652	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
14	nsv911801	chr19:42910416-42929502	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
15	nsv911802	chr19:42915110-42929254	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
16	nsv911803	chr19:42916841-42926406	Enhancers Weak transcription Active TSS Flanking Active TSS 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	6 gene(s)	inside rSNPs	diseases
17	nsv911804	chr19:42916841-42932699	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
18	nsv911805	chr19:42919405-42927065	Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
19	nsv911806	chr19:42919405-42928397	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
20	nsv911807	chr19:42920555-42929254	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42906200-42926200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr19:42906400-42926400	Weak transcription	Colonic Mucosa	Colon
3	chr19:42906600-42926400	Weak transcription	Fetal Lung	lung
4	chr19:42907400-42926600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:42909000-42925800	Weak transcription	Dnd41	blood
6	chr19:42912600-42925600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr19:42912800-42926200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr19:42913800-42925800	Weak transcription	NHDF-Ad	bronchial
9	chr19:42914000-42926400	Weak transcription	Ovary	ovary
10	chr19:42914400-42926000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr19:42915000-42925600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr19:42915200-42925800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr19:42917000-42926200	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr19:42917400-42926600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr19:42919000-42925800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr19:42922800-42926000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr19:42923000-42926200	Enhancers	Left Ventricle	heart
18	chr19:42923000-42926600	Enhancers	Spleen	Spleen
19	chr19:42923200-42926400	Enhancers	Esophagus	oesophagus
20	chr19:42923400-42926200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr19:42923400-42926400	Enhancers	Right Ventricle	heart
22	chr19:42923400-42926800	Enhancers	Fetal Muscle Leg	muscle
23	chr19:42923600-42925800	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr19:42923600-42925800	Enhancers	Brain Hippocampus Middle	brain
25	chr19:42923600-42926200	Enhancers	Brain Cingulate Gyrus	brain
26	chr19:42923600-42926200	Enhancers	Right Atrium	heart
27	chr19:42923600-42926400	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr19:42923600-42926600	Enhancers	HMEC	breast
29	chr19:42923600-42926800	Enhancers	Placenta	Placenta
30	chr19:42924000-42925600	Enhancers	Brain Substantia Nigra	brain
31	chr19:42924000-42926200	Enhancers	Brain Germinal Matrix	brain
32	chr19:42924000-42926400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr19:42924000-42926600	Enhancers	Primary T cells from cord blood	blood
34	chr19:42924000-42926600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
35	chr19:42924000-42927200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr19:42924200-42926000	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr19:42924200-42926000	Genic enhancers	Fetal Stomach	stomach
38	chr19:42924200-42926200	Enhancers	Brain Anterior Caudate	brain
39	chr19:42924200-42926400	Enhancers	Brain Angular Gyrus	brain
40	chr19:42924200-42926600	Enhancers	Primary T cells fromperipheralblood	blood
41	chr19:42924200-42926600	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr19:42924200-42926800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
43	chr19:42924200-42926800	Enhancers	Lung	lung
44	chr19:42924200-42927000	Enhancers	Pancreas	Pancrea
45	chr19:42924400-42925600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr19:42924400-42925600	Enhancers	Fetal Thymus	thymus
47	chr19:42924400-42925800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr19:42924400-42925800	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr19:42924400-42925800	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr19:42924400-42926200	Enhancers	Fetal Heart	heart

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