Variant report

Variant	rs3801012
Chromosome Location	chr7:5736390-5736391
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:5736261..5739455-chr7:5742456..5746657,4	MCF-7	breast:
2	chr7:5569883..5572115-chr7:5735560..5738502,2	MCF-7	breast:
3	chr7:5732435..5735665-chr7:5735782..5737442,3	K562	blood:
4	chr7:5734531..5737530-chr7:5742995..5745148,2	K562	blood:
5	chr7:5734503..5737746-chr7:5737831..5742522,7	MCF-7	breast:
6	chr7:5733734..5736608-chr7:5749498..5751681,2	K562	blood:
7	chr7:5465182..5466717-chr7:5734558..5737201,2	MCF-7	breast:
8	chr7:5736035..5737796-chr7:5742971..5745754,2	K562	blood:

Variant related genes	Relation type
ENSG00000075624	Chromatin interaction
ENSG00000272953	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs2345938	0.92[ASN][1000 genomes]
rs28380174	0.84[ASN][1000 genomes]
rs28519438	0.82[ASN][1000 genomes]
rs34865088	0.90[ASN][1000 genomes]
rs3801016	0.88[JPT][hapmap]
rs3807580	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57309152	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58364611	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58503972	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59086001	0.84[AFR][1000 genomes]
rs60181616	0.86[AFR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60372872	0.82[ASN][1000 genomes]
rs60442234	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60889993	0.84[AFR][1000 genomes]
rs61033429	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61210914	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61260366	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6463513	0.82[ASN][1000 genomes]
rs6944627	0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6951438	0.92[ASN][1000 genomes]
rs6956564	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6959871	1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs6969585	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6971289	1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs73339903	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73341604	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7795879	1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7806110	0.82[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7809733	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9648579	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9691118	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869165	chr7:4889618-5799719	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	352 gene(s)	inside rSNPs	diseases
2	nsv530979	chr7:5101631-5864814	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
3	nsv530981	chr7:5157150-5920006	Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	348 gene(s)	inside rSNPs	diseases
4	nsv530983	chr7:5370746-6070852	Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	368 gene(s)	inside rSNPs	diseases
5	nsv916391	chr7:5417945-5889565	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	336 gene(s)	inside rSNPs	diseases
6	nsv533108	chr7:5488018-6316581	Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	390 gene(s)	inside rSNPs	diseases
7	nsv482449	chr7:5557585-5743673	Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
8	nsv1033556	chr7:5565080-6186815	Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
9	nsv538710	chr7:5565080-6186815	Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers 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 miRNA target site	357 gene(s)	inside rSNPs	diseases
10	nsv530467	chr7:5617816-5815082	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
11	nsv1017612	chr7:5629728-5819144	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
12	nsv1021989	chr7:5629728-6186815	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
13	nsv887417	chr7:5667645-5760860	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
14	nsv887418	chr7:5675305-5772551	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
15	nsv887419	chr7:5703669-5820383	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
16	nsv1028652	chr7:5706207-5769489	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
17	nsv830891	chr7:5726301-5895460	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 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	chr7:5720200-5741400	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr7:5723000-5740800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr7:5723400-5740600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr7:5723400-5766400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr7:5723600-5740600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr7:5726000-5737000	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr7:5728600-5736600	Enhancers	Pancreas	Pancrea
8	chr7:5728600-5738200	Enhancers	Placenta	Placenta
9	chr7:5730000-5740400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr7:5730200-5736400	Flanking Active TSS	Colon Smooth Muscle	Colon
11	chr7:5730200-5736600	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr7:5730200-5738200	Enhancers	Ovary	ovary
13	chr7:5730400-5737000	Enhancers	Liver	Liver
14	chr7:5731400-5740800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr7:5731600-5736800	Enhancers	Spleen	Spleen
16	chr7:5731800-5737000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr7:5731800-5737000	Enhancers	Primary hematopoietic stem cells	blood
18	chr7:5732000-5740600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr7:5732000-5741000	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr7:5732400-5736800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr7:5732600-5747600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr7:5733400-5736800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr7:5733400-5740800	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr7:5733800-5736400	Weak transcription	Small Intestine	intestine
25	chr7:5733800-5738000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr7:5733800-5740400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr7:5734000-5736800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr7:5734000-5736800	Enhancers	Lung	lung
29	chr7:5734200-5736400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr7:5734200-5736600	Weak transcription	K562	blood
31	chr7:5734200-5736800	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr7:5734200-5739400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr7:5734200-5743400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr7:5734400-5738000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr7:5734400-5740400	Weak transcription	Gastric	stomach
36	chr7:5734600-5736400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr7:5734800-5736400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
38	chr7:5734800-5737200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr7:5734800-5738200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr7:5735000-5738400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr7:5735200-5736400	Enhancers	Fetal Intestine Large	intestine
42	chr7:5735200-5736400	Enhancers	HMEC	breast
43	chr7:5735200-5736600	Enhancers	Colonic Mucosa	Colon
44	chr7:5735200-5736800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr7:5735200-5736800	Enhancers	Fetal Muscle Trunk	muscle
46	chr7:5735200-5737000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr7:5735200-5737600	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr7:5735200-5738200	Enhancers	Left Ventricle	heart
49	chr7:5735200-5738400	Genic enhancers	Fetal Intestine Small	intestine
50	chr7:5735200-5738600	Enhancers	Right Atrium	heart

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