Variant report

Variant	rs1609813
Chromosome Location	chr4:3288220-3288221
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:3287264..3290154-chr4:3470213..3472155,2	MCF-7	breast:
2	chr4:3281505..3284592-chr4:3285630..3289153,4	MCF-7	breast:
3	chr4:3276746..3278804-chr4:3288196..3290777,2	K562	blood:
4	chr4:3287370..3290195-chr4:3296120..3298356,2	K562	blood:
5	chr4:3288141..3289800-chr4:3461769..3463366,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10019606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10022193	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10024540	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13118873	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13147370	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs13152190	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28652612	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4488885	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59898919	0.98[ASN][1000 genomes]
rs60551364	0.98[ASN][1000 genomes]
rs732869	0.89[CHB][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	nsv998290	chr4:3176454-3355758	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active 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	11 gene(s)	inside rSNPs	diseases
4	nsv878454	chr4:3215835-3305739	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv878455	chr4:3215835-3344891	Strong transcription Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS 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	10 gene(s)	inside rSNPs	diseases
6	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
7	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
8	nsv878458	chr4:3235518-3303976	Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
9	nsv878459	chr4:3235518-3310831	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
10	nsv878460	chr4:3260154-3303976	Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
11	nsv878461	chr4:3270488-3339038	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats 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	9 gene(s)	inside rSNPs	diseases
12	nsv593440	chr4:3283422-3339038	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
13	nsv461165	chr4:3283422-3342137	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
14	nsv593441	chr4:3283422-3342137	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 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	chr4:3286200-3292200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr4:3286800-3290600	Enhancers	Fetal Brain Male	brain
3	chr4:3287000-3288600	Enhancers	Spleen	Spleen
4	chr4:3287000-3288600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr4:3287000-3290200	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr4:3287000-3290800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
7	chr4:3287200-3288400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr4:3287200-3288600	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr4:3287200-3288800	Enhancers	HMEC	breast
10	chr4:3287200-3289000	Enhancers	Primary hematopoietic stem cells	blood
11	chr4:3287200-3289600	Bivalent Enhancer	Fetal Stomach	stomach
12	chr4:3287400-3288600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr4:3287400-3288800	Enhancers	Primary B cells from cord blood	blood
14	chr4:3287600-3288400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr4:3287600-3288400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr4:3287600-3288400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr4:3287600-3288400	Bivalent Enhancer	Colonic Mucosa	Colon
18	chr4:3287600-3288400	Enhancers	Pancreas	Pancrea
19	chr4:3287600-3288400	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
20	chr4:3287600-3288400	Flanking Active TSS	Osteobl	bone
21	chr4:3287600-3288600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr4:3287600-3288600	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:3287600-3288600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr4:3287600-3288600	Enhancers	Placenta Amnion	Placenta Amnion
25	chr4:3287600-3288800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
26	chr4:3287600-3288800	Enhancers	Esophagus	oesophagus
27	chr4:3287600-3288800	Bivalent/Poised TSS	HepG2	liver
28	chr4:3287600-3289400	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr4:3287600-3289600	Enhancers	Fetal Lung	lung
30	chr4:3287600-3289800	Enhancers	Ovary	ovary
31	chr4:3287600-3290000	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr4:3287600-3290200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr4:3287600-3290400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr4:3287600-3290400	Bivalent Enhancer	Fetal Muscle Leg	muscle
35	chr4:3287600-3291000	Enhancers	Brain Germinal Matrix	brain
36	chr4:3287800-3288400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr4:3287800-3288400	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
38	chr4:3287800-3288600	Flanking Active TSS	GM12878-XiMat	blood
39	chr4:3287800-3289000	Enhancers	Primary B cells from peripheral blood	blood
40	chr4:3287800-3289400	Enhancers	Placenta	Placenta
41	chr4:3287800-3289400	Bivalent Enhancer	Fetal Thymus	thymus
42	chr4:3287800-3289600	Enhancers	Brain Hippocampus Middle	brain
43	chr4:3287800-3289600	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr4:3287800-3290200	Enhancers	Fetal Brain Female	brain
45	chr4:3288000-3288400	Bivalent Enhancer	Duodenum Mucosa	Duodenum
46	chr4:3288000-3288600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr4:3288000-3288600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr4:3288000-3288600	Enhancers	NHDF-Ad	bronchial
49	chr4:3288000-3288800	Enhancers	Skeletal Muscle Female	skeletal muscle
50	chr4:3288000-3289000	Enhancers	Primary monocytes fromperipheralblood	blood

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