Variant report

Variant	rs1613413
Chromosome Location	chr1:92178260-92178261
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	IRF1	chr1:92177976-92179059	K562	blood:	n/a	chr1:92178145-92178158 chr1:92178144-92178155 chr1:92178142-92178156 chr1:92178145-92178158 chr1:92178140-92178157
2	EBF1	chr1:92178023-92178410	GM12878	blood:	n/a	n/a
3	MXI1	chr1:92178119-92178268	GM12878	blood:	n/a	n/a
4	IRF1	chr1:92177790-92178560	K562	blood:	n/a	chr1:92178145-92178158 chr1:92178144-92178155 chr1:92178142-92178156 chr1:92178145-92178158 chr1:92178140-92178157

Variant related genes	Relation type
TGFBR3	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10157635	0.88[EUR][1000 genomes]
rs10157887	0.95[EUR][1000 genomes]
rs10874909	0.84[EUR][1000 genomes]
rs12060235	0.88[EUR][1000 genomes]
rs12065370	0.95[EUR][1000 genomes]
rs17131536	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17131541	0.88[EUR][1000 genomes]
rs2810889	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2810890	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs284866	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs284867	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs284868	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs284869	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs284871	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs284872	0.85[ASN][1000 genomes]
rs284875	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs284878	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][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	nsv1009560	chr1:91897078-92270781	Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats 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	14 gene(s)	inside rSNPs	diseases
2	nsv1012864	chr1:92067100-92827761	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv535029	chr1:92067100-92827761	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	esv2763581	chr1:92068967-92203803	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv1014990	chr1:92084142-92206674	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv530438	chr1:92091957-92827760	Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv1010179	chr1:92140209-92655952	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv535030	chr1:92140209-92655952	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92152600-92184200	Strong transcription	HepG2	liver
2	chr1:92153000-92197000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:92155400-92178800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr1:92155600-92178800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr1:92155800-92191200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:92159800-92183800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr1:92164000-92184400	Weak transcription	Hela-S3	cervix
8	chr1:92164000-92195000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr1:92165400-92178600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr1:92165400-92178600	Weak transcription	Fetal Brain Male	brain
11	chr1:92165800-92184800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr1:92165800-92196800	Weak transcription	Small Intestine	intestine
13	chr1:92166600-92191000	Weak transcription	Brain Hippocampus Middle	brain
14	chr1:92167400-92184800	Weak transcription	A549	lung
15	chr1:92168000-92178600	Weak transcription	Osteobl	bone
16	chr1:92168000-92191000	Weak transcription	HUVEC	blood vessel
17	chr1:92169200-92178800	Strong transcription	Liver	Liver
18	chr1:92169800-92187200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:92171000-92196800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr1:92171200-92196800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr1:92171800-92178600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr1:92172200-92178600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:92172200-92178600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:92172200-92178600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr1:92172800-92197000	Weak transcription	Colonic Mucosa	Colon
26	chr1:92173000-92178600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr1:92173200-92182400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr1:92173200-92202400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr1:92173600-92178600	Weak transcription	HSMMtube	muscle
30	chr1:92173600-92185000	Weak transcription	Gastric	stomach
31	chr1:92173600-92197800	Weak transcription	Brain Angular Gyrus	brain
32	chr1:92173800-92178600	Weak transcription	Fetal Thymus	thymus
33	chr1:92173800-92184400	Weak transcription	Fetal Intestine Small	intestine
34	chr1:92173800-92184600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr1:92174400-92180200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:92174400-92181600	Weak transcription	Pancreas	Pancrea
37	chr1:92174400-92184400	Weak transcription	Esophagus	oesophagus
38	chr1:92174400-92191200	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr1:92174600-92178600	Weak transcription	Brain Anterior Caudate	brain
40	chr1:92174600-92180200	Weak transcription	Spleen	Spleen
41	chr1:92174600-92184800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr1:92175400-92180600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr1:92176000-92178400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr1:92176400-92178400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr1:92176600-92179400	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:92176800-92178600	Weak transcription	Aorta	Aorta
47	chr1:92176800-92178600	Weak transcription	Psoas Muscle	Psoas
48	chr1:92176800-92184400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr1:92177200-92179400	Flanking Active TSS	GM12878-XiMat	blood
50	chr1:92177600-92178400	Genic enhancers	Fetal Heart	heart

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