Variant report

Variant	rs1661960
Chromosome Location	chr19:53473390-53473391
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:53425712..53428139-chr19:53470752..53473566,2	MCF-7	breast:
2	chr19:53465551..53467815-chr19:53472678..53475651,2	K562	blood:

Variant related genes	Relation type
ENSG00000221874	Chromatin interaction
ENSG00000269646	Chromatin interaction
ENSG00000180257	Chromatin interaction
ENSG00000213793	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12709932	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12972188	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12979823	0.94[EUR][1000 genomes]
rs1650957	0.94[EUR][1000 genomes]
rs1650959	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1650960	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1650961	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1650963	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1650964	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1650966	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1661957	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1661958	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1661959	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16984219	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34983575	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3848564	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9304743	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9967593	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][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	nsv1066762	chr19:53112568-53552217	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv432072	chr19:53144788-53554388	Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv3401212	chr19:53151131-53482063	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1058903	chr19:53193570-53489633	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv1067280	chr19:53193570-53567287	Active TSS Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv544062	chr19:53193570-53567287	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv580030	chr19:53194344-53547394	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv1057118	chr19:53195426-53480449	Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv530807	chr19:53210488-53695881	Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking 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 target site	43 gene(s)	inside rSNPs	diseases
10	esv3431689	chr19:53291230-53483998	Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
11	nsv912330	chr19:53317001-53478109	Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Enhancers 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 target site	18 gene(s)	inside rSNPs	diseases
12	nsv1064234	chr19:53346827-53480449	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers 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	16 gene(s)	inside rSNPs	diseases
13	esv3326632	chr19:53371248-53697569	Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
14	nsv963071	chr19:53401720-53480869	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
15	esv2758506	chr19:53410459-53652575	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
16	esv2758769	chr19:53410459-53652575	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
17	nsv428370	chr19:53410459-53652575	Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
18	esv2757701	chr19:53470514-53554240	Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:53467000-53479000	Weak transcription	Brain Substantia Nigra	brain
2	chr19:53467000-53489000	Weak transcription	Right Ventricle	heart
3	chr19:53467000-53494600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr19:53467200-53478800	Weak transcription	Thymus	Thymus
5	chr19:53467200-53480000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr19:53467200-53488600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr19:53467200-53489200	Weak transcription	Colon Smooth Muscle	Colon
8	chr19:53467200-53495400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr19:53467400-53481800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr19:53470400-53474200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr19:53470400-53475200	Strong transcription	Placenta	Placenta
12	chr19:53470800-53476600	Weak transcription	Fetal Stomach	stomach
13	chr19:53471000-53474600	Weak transcription	Fetal Intestine Large	intestine
14	chr19:53471000-53481600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr19:53471200-53481200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr19:53471400-53475400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr19:53471600-53474000	Strong transcription	Fetal Kidney	kidney
18	chr19:53471600-53474400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
19	chr19:53471600-53475600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr19:53471600-53487600	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr19:53471800-53474000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr19:53471800-53474000	Strong transcription	Fetal Lung	lung
23	chr19:53472000-53474000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr19:53472000-53474200	Strong transcription	Ovary	ovary
25	chr19:53472000-53474200	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr19:53472000-53474800	Strong transcription	Left Ventricle	heart
27	chr19:53472000-53475000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr19:53472000-53475000	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
29	chr19:53472200-53473400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr19:53472200-53473800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
31	chr19:53472200-53473800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
32	chr19:53472200-53474200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr19:53472200-53478000	Weak transcription	Right Atrium	heart
34	chr19:53472400-53473600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr19:53472400-53473800	Strong transcription	Placenta Amnion	Placenta Amnion
36	chr19:53472400-53474200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
37	chr19:53472600-53473400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr19:53472600-53475400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr19:53472600-53489000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr19:53472800-53474200	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr19:53472800-53474200	Strong transcription	HUVEC	blood vessel
42	chr19:53472800-53474600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr19:53472800-53474800	Weak transcription	Spleen	Spleen
44	chr19:53472800-53476000	Weak transcription	Esophagus	oesophagus
45	chr19:53472800-53478000	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr19:53472800-53478000	Weak transcription	Aorta	Aorta
47	chr19:53472800-53481600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr19:53472800-53481600	Weak transcription	Gastric	stomach
49	chr19:53472800-53487800	Weak transcription	Adipose Nuclei	Adipose
50	chr19:53472800-53495800	Weak transcription	Brain Inferior Temporal Lobe	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links