Variant report

Variant	rs1962840
Chromosome Location	chr4:119753199-119753200
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:119749704..119751469-chr4:119751998..119754099,2	K562	blood:
2	chr4:119749856..119753321-chr4:119754214..119757682,4	MCF-7	breast:
3	chr4:119733285..119736755-chr4:119749936..119754070,3	K562	blood:

Variant related genes	Relation type
ENSG00000150961	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1019696	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11098453	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11098459	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11098460	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12512594	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12643205	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13112913	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13139244	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1365549	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1365550	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1365551	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2114461	0.82[ASN][1000 genomes]
rs2303512	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2389688	0.96[ASN][1000 genomes]
rs34057511	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35934778	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36096663	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3775839	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3775840	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4833592	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4833593	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4834704	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4834705	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4834706	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6811006	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6817084	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7375858	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519017	chr4:118828807-119771481	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv3355840	chr4:119296640-119774737	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv516777	chr4:119733366-119762951	Strong transcription Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:119718400-119756000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr4:119718600-119753600	Weak transcription	Fetal Heart	heart
3	chr4:119719000-119756200	Weak transcription	Fetal Brain Male	brain
4	chr4:119732000-119755800	Weak transcription	Brain Angular Gyrus	brain
5	chr4:119733400-119753200	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr4:119734800-119755800	Weak transcription	Thymus	Thymus
7	chr4:119735600-119756000	Weak transcription	Brain Anterior Caudate	brain
8	chr4:119735600-119756200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr4:119736400-119756200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr4:119736800-119755800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr4:119736800-119756200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr4:119736800-119756200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr4:119736800-119756200	Weak transcription	Brain Substantia Nigra	brain
14	chr4:119737000-119755800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr4:119737000-119756000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr4:119744800-119753400	Weak transcription	Primary hematopoietic stem cells	blood
17	chr4:119744800-119753400	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr4:119744800-119755800	Weak transcription	Brain Hippocampus Middle	brain
19	chr4:119745200-119753400	Weak transcription	Spleen	Spleen
20	chr4:119745200-119755400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr4:119745400-119754800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr4:119746000-119753400	Weak transcription	Colonic Mucosa	Colon
23	chr4:119746000-119753600	Weak transcription	Primary B cells from peripheral blood	blood
24	chr4:119746000-119754800	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr4:119746200-119754800	Weak transcription	Small Intestine	intestine
26	chr4:119746600-119753400	Weak transcription	Primary B cells from cord blood	blood
27	chr4:119748000-119754600	Genic enhancers	HepG2	liver
28	chr4:119748200-119754800	Strong transcription	Fetal Muscle Trunk	muscle
29	chr4:119748200-119755000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr4:119748200-119755400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr4:119748400-119753200	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr4:119748400-119753400	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr4:119748400-119755800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr4:119748600-119754200	Weak transcription	Right Atrium	heart
35	chr4:119748600-119754600	Strong transcription	HSMM	muscle
36	chr4:119748600-119756200	Weak transcription	Psoas Muscle	Psoas
37	chr4:119749000-119753400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr4:119749000-119753600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr4:119749000-119754000	Strong transcription	Fetal Stomach	stomach
40	chr4:119749000-119754200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr4:119749000-119755200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr4:119749000-119755400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr4:119749000-119755600	Weak transcription	Hela-S3	cervix
44	chr4:119749000-119756200	Weak transcription	Esophagus	oesophagus
45	chr4:119749200-119754000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr4:119749200-119755000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr4:119749200-119755000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr4:119749200-119755200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr4:119749200-119755800	Weak transcription	A549	lung
50	chr4:119749400-119754200	Strong transcription	Primary T cells fromperipheralblood	blood

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