Variant report

Variant	rs2941665
Chromosome Location	chr5:126146864-126146865
allele	A/C
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	GATA1	chr5:126146585-126148220	PBDE	blood:	n/a	chr5:126147163-126147179 chr5:126148077-126148098 chr5:126148079-126148095 chr5:126148098-126148107
2	POLR2A	chr5:126145092-126148371	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:126144524..126147044-chr5:126151207..126155375,3	MCF-7	breast:
2	chr5:126145493..126147146-chr5:126147847..126149410,2	MCF-7	breast:
3	chr5:126135601..126137322-chr5:126144015..126147273,3	K562	blood:
4	chr5:126112758..126116358-chr5:126145679..126148817,3	K562	blood:
5	chr5:126139495..126141394-chr5:126144830..126147381,2	K562	blood:

Variant related genes	Relation type
LMNB1	TF binding region
ENSG00000113368	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1510955	0.93[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2036844	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2271354	0.81[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2941662	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2941667	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2973584	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2973585	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2973586	0.83[CHB][hapmap];0.90[CHD][hapmap]
rs2973599	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2973602	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2973603	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2973888	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2973891	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2973892	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6895856	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs959573	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949054	chr5:125918148-126254480	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv534292	chr5:125993451-126259315	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer 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	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126114600-126161600	Weak transcription	Ovary	ovary
2	chr5:126116600-126147800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr5:126130400-126165800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr5:126132200-126161200	Weak transcription	Gastric	stomach
5	chr5:126135200-126147200	Weak transcription	Fetal Brain Male	brain
6	chr5:126136000-126175200	Strong transcription	Dnd41	blood
7	chr5:126136400-126162400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr5:126137600-126154600	Weak transcription	Fetal Kidney	kidney
9	chr5:126137600-126166600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr5:126137800-126147400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr5:126139800-126148200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr5:126139800-126160600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr5:126139800-126175400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr5:126140000-126150600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr5:126140000-126162000	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr5:126140000-126162200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr5:126140000-126175200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr5:126140000-126175400	Strong transcription	Fetal Thymus	thymus
19	chr5:126140200-126150600	Strong transcription	Thymus	Thymus
20	chr5:126140200-126161400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr5:126140200-126161800	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr5:126140200-126162600	Weak transcription	Colonic Mucosa	Colon
23	chr5:126140200-126163400	Weak transcription	Pancreas	Pancrea
24	chr5:126140400-126147200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr5:126140400-126150000	Strong transcription	Fetal Muscle Leg	muscle
26	chr5:126140400-126150600	Strong transcription	Fetal Muscle Trunk	muscle
27	chr5:126140400-126161200	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr5:126140400-126161800	Weak transcription	Placenta	Placenta
29	chr5:126140400-126162200	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr5:126140600-126161600	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr5:126140800-126161400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr5:126141000-126147600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr5:126141000-126159200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr5:126141000-126177400	Weak transcription	Small Intestine	intestine
35	chr5:126141200-126147600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr5:126141200-126161400	Weak transcription	Lung	lung
37	chr5:126141200-126181800	Weak transcription	Rectal Smooth Muscle	rectum
38	chr5:126141400-126147600	Weak transcription	Brain Angular Gyrus	brain
39	chr5:126141400-126150400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr5:126141400-126174200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr5:126141600-126150600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr5:126141600-126150600	Strong transcription	Fetal Stomach	stomach
43	chr5:126141600-126162200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr5:126141600-126167400	Weak transcription	Brain Substantia Nigra	brain
45	chr5:126142000-126149200	Strong transcription	Hela-S3	cervix
46	chr5:126142400-126147400	Weak transcription	Fetal Lung	lung
47	chr5:126142400-126147600	Weak transcription	NHDF-Ad	bronchial
48	chr5:126142600-126147400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr5:126142600-126161200	Weak transcription	Spleen	Spleen
50	chr5:126142800-126147400	Weak transcription	Fetal Intestine Large	intestine

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