Variant report

Variant	rs16844197
Chromosome Location	chr4:3366560-3366561
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:3365147..3366815-chr4:3405868..3408460,2	MCF-7	breast:
2	chr4:3365608..3368928-chr4:3369932..3375344,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159788	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs12640186	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12640526	0.92[ASN][1000 genomes]
rs12640721	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12643903	0.95[CHB][hapmap];0.89[ASN][1000 genomes]
rs16844201	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2073286	0.95[CHB][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2281470	0.95[CHB][hapmap];0.89[ASN][1000 genomes]
rs2343799	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2749775	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2749776	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2749779	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2749786	0.95[CEU][hapmap];0.90[CHB][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2857859	0.90[CEU][hapmap];0.95[CHB][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2857860	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3129329	1.00[CEU][hapmap];0.91[CHB][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3129330	0.90[CEU][hapmap];0.90[CHB][hapmap];0.82[ASN][1000 genomes]
rs3129331	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3129332	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3129333	0.94[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3129336	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58949283	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62274923	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62274924	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73193371	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73193372	0.87[ASN][1000 genomes]
rs881818	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[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	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking 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	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats 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	63 gene(s)	inside rSNPs	diseases
3	nsv878456	chr4:3215835-3467519	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv428106	chr4:3226182-3752322	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv878462	chr4:3311548-3505448	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv1007847	chr4:3317904-3527357	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv537001	chr4:3317904-3527357	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv878463	chr4:3363994-3498896	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3334000-3370600	Weak transcription	Right Atrium	heart
2	chr4:3344400-3367600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr4:3348200-3367400	Weak transcription	Fetal Heart	heart
4	chr4:3348400-3367600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr4:3350800-3367600	Weak transcription	Ovary	ovary
6	chr4:3354800-3368200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr4:3355000-3367800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr4:3355200-3368400	Weak transcription	Fetal Intestine Small	intestine
9	chr4:3356600-3368000	Weak transcription	Fetal Intestine Large	intestine
10	chr4:3358200-3367800	Weak transcription	HepG2	liver
11	chr4:3358800-3369000	Weak transcription	Fetal Lung	lung
12	chr4:3360400-3370000	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr4:3360600-3370000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr4:3361400-3370000	Weak transcription	HSMM	muscle
15	chr4:3362800-3369200	Weak transcription	HSMMtube	muscle
16	chr4:3363600-3368400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr4:3363600-3371000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr4:3364400-3366800	Enhancers	Brain Germinal Matrix	brain
19	chr4:3364600-3366600	Enhancers	Fetal Muscle Trunk	muscle
20	chr4:3364600-3367000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr4:3364800-3367200	Weak transcription	Fetal Kidney	kidney
22	chr4:3364800-3368400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr4:3364800-3370400	Weak transcription	Pancreas	Pancrea
24	chr4:3364800-3370400	Weak transcription	NHLF	lung
25	chr4:3364800-3370600	Weak transcription	Esophagus	oesophagus
26	chr4:3365000-3366600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr4:3365000-3367000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr4:3365000-3367000	Enhancers	Fetal Muscle Leg	muscle
29	chr4:3365000-3367600	Weak transcription	Right Ventricle	heart
30	chr4:3365000-3369000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr4:3365000-3371000	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr4:3365200-3366600	Enhancers	Primary hematopoietic stem cells	blood
33	chr4:3365200-3366600	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr4:3365400-3368200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr4:3365400-3368400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr4:3365600-3366800	Enhancers	Brain Hippocampus Middle	brain
37	chr4:3365600-3367200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr4:3365600-3370400	Weak transcription	Gastric	stomach
39	chr4:3365800-3366800	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr4:3365800-3367000	Weak transcription	Fetal Brain Male	brain
41	chr4:3365800-3370000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr4:3365800-3370000	Weak transcription	Duodenum Mucosa	Duodenum
43	chr4:3366000-3367000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr4:3366000-3367200	Enhancers	Brain Anterior Caudate	brain
45	chr4:3366000-3367800	Weak transcription	Fetal Stomach	stomach
46	chr4:3366000-3368800	Enhancers	Liver	Liver
47	chr4:3366000-3369000	Weak transcription	Fetal Thymus	thymus
48	chr4:3366000-3370200	Weak transcription	Primary T cells from cord blood	blood
49	chr4:3366000-3370400	Weak transcription	Thymus	Thymus
50	chr4:3366000-3370600	Weak transcription	Colonic Mucosa	Colon

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