Variant report

Variant	rs3742190
Chromosome Location	chr13:111175718-111175719
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:111173040..111177244-chr13:111365856..111368723,3	MCF-7	breast:
2	chr13:111160160..111164294-chr13:111174560..111180121,5	MCF-7	breast:
3	chr13:111175089..111177508-chr13:111178295..111180453,3	MCF-7	breast:
4	chr13:111162545..111165671-chr13:111172658..111175880,3	MCF-7	breast:
5	chr13:111175360..111178796-chr13:111180023..111183032,3	MCF-7	breast:
6	chr13:111107007..111108826-chr13:111174960..111176925,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000153487	Chromatin interaction
ENSG00000232814	Chromatin interaction
ENSG00000134905	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10047685	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10220027	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1059289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2296846	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038914	chr13:110860219-111190104	Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv1046423	chr13:110936104-111286607	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv832720	chr13:111100235-111295993	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv1046291	chr13:111125747-111257861	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv1045143	chr13:111126822-111242791	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv901009	chr13:111134780-111176393	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv1044234	chr13:111143053-111370580	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	216 gene(s)	inside rSNPs	diseases
8	nsv949634	chr13:111151460-111582996	Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
9	nsv984479	chr13:111157297-111176429	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	n/a
10	nsv901010	chr13:111165390-111286592	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
11	nsv1053922	chr13:111167764-111330876	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats 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	25 gene(s)	inside rSNPs	diseases
12	nsv1043849	chr13:111167764-111340418	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
13	nsv541924	chr13:111167764-111340418	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats 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	25 gene(s)	inside rSNPs	diseases
14	nsv1036160	chr13:111167764-111347308	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
15	nsv541925	chr13:111167764-111347308	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS 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	25 gene(s)	inside rSNPs	diseases
16	nsv901011	chr13:111168951-111280002	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:111159600-111176800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr13:111160800-111176400	Weak transcription	Psoas Muscle	Psoas
3	chr13:111160800-111209600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr13:111162600-111177200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr13:111165400-111179800	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr13:111165600-111176400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr13:111165600-111176600	Weak transcription	HMEC	breast
8	chr13:111165800-111179400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr13:111166600-111176800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr13:111167000-111190800	Weak transcription	Fetal Kidney	kidney
11	chr13:111167200-111179600	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr13:111167400-111176800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr13:111169600-111178600	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr13:111171400-111176200	Weak transcription	Hela-S3	cervix
15	chr13:111171400-111176600	Weak transcription	K562	blood
16	chr13:111171400-111178200	Enhancers	Fetal Brain Male	brain
17	chr13:111172200-111176200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr13:111173000-111180000	Enhancers	Right Atrium	heart
19	chr13:111173400-111175800	Enhancers	Liver	Liver
20	chr13:111173400-111176800	Strong transcription	Fetal Stomach	stomach
21	chr13:111173400-111183200	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr13:111173600-111176400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr13:111173600-111176800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr13:111173600-111176800	Weak transcription	Esophagus	oesophagus
25	chr13:111173600-111176800	Weak transcription	Ovary	ovary
26	chr13:111173600-111179600	Weak transcription	Fetal Lung	lung
27	chr13:111173800-111176600	Weak transcription	Colon Smooth Muscle	Colon
28	chr13:111173800-111176600	Weak transcription	HSMMtube	muscle
29	chr13:111173800-111176800	Weak transcription	Rectal Smooth Muscle	rectum
30	chr13:111173800-111180000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr13:111174000-111175800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr13:111174000-111175800	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr13:111174000-111176600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr13:111174000-111176800	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr13:111174000-111176800	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr13:111174000-111176800	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr13:111174000-111176800	Weak transcription	HSMM	muscle
38	chr13:111174000-111177200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr13:111174000-111179800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr13:111174200-111177000	Weak transcription	Primary B cells from cord blood	blood
41	chr13:111174200-111177000	Weak transcription	Brain Hippocampus Middle	brain
42	chr13:111174200-111177600	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr13:111174400-111175800	Weak transcription	Primary hematopoietic stem cells	blood
44	chr13:111174400-111176600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr13:111174400-111178000	Enhancers	Aorta	Aorta
46	chr13:111174600-111175800	Weak transcription	Small Intestine	intestine
47	chr13:111174600-111176000	Weak transcription	Stomach Mucosa	stomach
48	chr13:111174600-111176200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr13:111174600-111176600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr13:111174600-111176600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links