Variant report

Variant	rs13405842
Chromosome Location	chr2:97258451-97258452
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:97257494..97261086-chr2:97426493..97430081,3	MCF-7	breast:
2	chr2:97249969..97252085-chr2:97258297..97259970,2	K562	blood:
3	chr2:97258239..97260866-chr2:97265002..97267473,2	K562	blood:
4	chr2:97257801..97260638-chr2:97301331..97305337,3	K562	blood:

Variant related genes	Relation type
ENSG00000158158	Chromatin interaction
ENSG00000114982	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10175415	0.83[AFR][1000 genomes]
rs10183164	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10185002	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10199227	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10203766	0.91[AFR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10209315	0.82[ASN][1000 genomes]
rs13384114	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13389475	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13393729	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13395011	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13398740	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292942	0.89[EUR][1000 genomes]
rs35715176	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55687728	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55716397	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs59398186	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59426746	0.89[EUR][1000 genomes]
rs60326991	0.93[ASN][1000 genomes]
rs61063398	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6718340	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6732115	0.90[JPT][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6733589	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6753713	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72939379	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72941209	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72941214	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72941219	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72941235	0.83[EUR][1000 genomes]
rs747757	0.99[AFR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7604736	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7607990	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933671	chr2:96739308-97652262	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv1000780	chr2:96740430-97671395	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv535826	chr2:96740430-97671395	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
4	nsv874677	chr2:96756547-97717345	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
5	nsv1001204	chr2:96766559-97728507	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
6	nsv535827	chr2:96766559-97728507	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS 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 miRNA target site	162 gene(s)	inside rSNPs	diseases
7	esv3460902	chr2:97138421-97459342	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	esv3460903	chr2:97138421-97459342	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
9	nsv999871	chr2:97157196-97407711	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS 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 lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv535829	chr2:97157196-97407711	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
11	nsv469775	chr2:97240926-97412491	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
12	nsv482586	chr2:97240926-97412491	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
13	nsv834306	chr2:97241115-97412938	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers 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 lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97239600-97258800	Weak transcription	Right Ventricle	heart
2	chr2:97244800-97259400	Weak transcription	Stomach Mucosa	stomach
3	chr2:97246800-97258800	Weak transcription	Pancreas	Pancrea
4	chr2:97246800-97259200	Weak transcription	Fetal Brain Male	brain
5	chr2:97247200-97259200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr2:97248400-97260000	Weak transcription	Colonic Mucosa	Colon
7	chr2:97248400-97283600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr2:97248800-97266200	Weak transcription	Small Intestine	intestine
9	chr2:97249200-97258800	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr2:97249200-97258800	Weak transcription	NHLF	lung
11	chr2:97249600-97258600	Weak transcription	Fetal Kidney	kidney
12	chr2:97251200-97259000	Weak transcription	HUVEC	blood vessel
13	chr2:97251600-97259000	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr2:97253200-97259000	Weak transcription	Esophagus	oesophagus
15	chr2:97253200-97259200	Weak transcription	HSMM	muscle
16	chr2:97253200-97266200	Weak transcription	Right Atrium	heart
17	chr2:97253600-97259000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr2:97253800-97258800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr2:97254200-97258800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr2:97254800-97271000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr2:97255000-97267800	Strong transcription	A549	lung
22	chr2:97255200-97259000	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr2:97255200-97263800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr2:97255400-97258800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr2:97255400-97258800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr2:97255600-97259000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:97256000-97259400	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr2:97256000-97262200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr2:97256000-97264600	Strong transcription	Fetal Intestine Small	intestine
30	chr2:97256200-97282400	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr2:97256400-97258600	Weak transcription	Rectal Smooth Muscle	rectum
32	chr2:97256400-97258800	Weak transcription	Hela-S3	cervix
33	chr2:97256600-97258600	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr2:97256600-97259000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr2:97256600-97274200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr2:97256600-97283800	Strong transcription	Placenta	Placenta
37	chr2:97256600-97287000	Strong transcription	Dnd41	blood
38	chr2:97256800-97258600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr2:97256800-97258800	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr2:97256800-97262800	Strong transcription	Fetal Brain Female	brain
41	chr2:97256800-97263800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr2:97256800-97267000	Strong transcription	Liver	Liver
43	chr2:97256800-97274200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr2:97257000-97258600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr2:97257000-97262600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr2:97257000-97264200	Strong transcription	Primary B cells from cord blood	blood
47	chr2:97257000-97264200	Strong transcription	Fetal Muscle Trunk	muscle
48	chr2:97257000-97267200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr2:97257000-97279600	Strong transcription	Fetal Lung	lung
50	chr2:97257200-97258800	Strong transcription	Primary T helper cells fromperipheralblood	blood

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