Variant report

Variant	rs11084440
Chromosome Location	chr19:56782965-56782966
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	POLR2A	chr19:56781926-56783021	HL-60	blood:	n/a	n/a
2	FOS	chr19:56782926-56782995	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr19:56782702-56783212	K562	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000267710	TF binding region
ZSCAN5A	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10775568	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11667369	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11670857	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11670870	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11672079	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11672081	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11672220	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11673002	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11883295	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs12460523	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12461130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17273365	0.85[CEU][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2869158	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3205192	0.85[CEU][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57090480	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57731201	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58815584	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59503198	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59565427	0.91[EUR][1000 genomes]
rs59820036	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62122532	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62122534	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62122536	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7247765	0.84[JPT][hapmap]
rs7252570	0.86[CEU][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73069662	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs755058	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs758758	0.85[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs758760	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8101809	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8103418	0.86[CEU][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8104291	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs965567	0.89[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	nsv1064371	chr19:56418215-56842450	ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
2	nsv1057316	chr19:56418215-56849458	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
3	nsv912516	chr19:56601298-56981382	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases
4	nsv1058152	chr19:56703368-56805035	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv544093	chr19:56703368-56805035	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv526325	chr19:56741186-56852035	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv949121	chr19:56754719-57591038	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
8	nsv528817	chr19:56779041-56785408	Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56729200-56803000	Weak transcription	Pancreas	Pancrea
2	chr19:56753000-56809000	Weak transcription	Gastric	stomach
3	chr19:56764200-56788400	Weak transcription	A549	lung
4	chr19:56764400-56788400	Weak transcription	Fetal Muscle Leg	muscle
5	chr19:56764400-56788600	Weak transcription	Duodenum Mucosa	Duodenum
6	chr19:56764400-56798600	Weak transcription	Placenta	Placenta
7	chr19:56764600-56788200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr19:56764600-56799400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr19:56764600-56804000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr19:56765000-56788400	Weak transcription	Brain Anterior Caudate	brain
11	chr19:56766600-56804200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr19:56768600-56794800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr19:56768800-56783800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr19:56769200-56788400	Weak transcription	Adipose Nuclei	Adipose
15	chr19:56770200-56795200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr19:56770200-56799400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr19:56770400-56804400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr19:56771200-56787200	Weak transcription	Liver	Liver
19	chr19:56771200-56788400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr19:56771200-56792000	Weak transcription	Aorta	Aorta
21	chr19:56771400-56817200	Weak transcription	Fetal Brain Male	brain
22	chr19:56771600-56807000	Weak transcription	Right Ventricle	heart
23	chr19:56772000-56788400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr19:56772400-56788400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr19:56772800-56784400	Weak transcription	Stomach Smooth Muscle	stomach
26	chr19:56772800-56788400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr19:56772800-56807600	Weak transcription	Primary hematopoietic stem cells	blood
28	chr19:56772800-56824200	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr19:56773000-56788200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr19:56773000-56807400	Weak transcription	Esophagus	oesophagus
31	chr19:56773600-56790000	Weak transcription	Primary B cells from cord blood	blood
32	chr19:56774200-56788400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr19:56775000-56783800	Weak transcription	Primary T cells from cord blood	blood
34	chr19:56775000-56784800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr19:56775800-56815600	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr19:56777000-56792800	Weak transcription	Fetal Intestine Large	intestine
37	chr19:56779600-56820200	Weak transcription	Hela-S3	cervix
38	chr19:56779800-56800000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr19:56779800-56807200	Weak transcription	Left Ventricle	heart
40	chr19:56781000-56783400	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr19:56781400-56804600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr19:56781600-56783200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
43	chr19:56781800-56783200	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr19:56782000-56783000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr19:56782200-56783200	Enhancers	Brain Germinal Matrix	brain
46	chr19:56782200-56784200	Enhancers	Muscle Satellite Cultured Cells	--
47	chr19:56782200-56799200	Weak transcription	Fetal Intestine Small	intestine
48	chr19:56782400-56783000	Enhancers	Fetal Stomach	stomach
49	chr19:56782400-56783000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
50	chr19:56782400-56783600	Weak transcription	HUVEC	blood vessel

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