Variant report

Variant	rs2139406
Chromosome Location	chr2:97366779-97366780
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:97361665..97367083-chr2:97369307..97373546,6	K562	blood:
2	chr2:97365576..97367598-chr2:97371626..97373546,2	K562	blood:
3	chr2:97302224..97304298-chr2:97365306..97367348,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114982	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs1320146	1.00[GIH][hapmap]
rs17119562	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs17119564	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.96[EUR][1000 genomes]
rs17119591	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs17119598	1.00[GIH][hapmap]
rs2276654	1.00[GIH][hapmap]
rs2280356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2314399	0.96[EUR][1000 genomes]
rs2872633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3731940	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.96[EUR][1000 genomes]
rs3731941	1.00[GIH][hapmap]
rs56913233	0.96[EUR][1000 genomes]
rs57582887	0.96[EUR][1000 genomes]
rs59073958	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59648446	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61742095	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61750875	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62152766	0.96[EUR][1000 genomes]
rs62152767	0.96[EUR][1000 genomes]
rs62152771	0.96[EUR][1000 genomes]
rs62152780	0.96[EUR][1000 genomes]
rs62152787	0.96[EUR][1000 genomes]
rs62156206	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62156207	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62156208	0.96[EUR][1000 genomes]
rs62156209	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62156210	0.96[EUR][1000 genomes]
rs62156211	0.96[EUR][1000 genomes]
rs62156212	0.96[EUR][1000 genomes]
rs62156213	0.96[EUR][1000 genomes]
rs62156216	0.96[EUR][1000 genomes]
rs62156219	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62156220	0.96[EUR][1000 genomes]
rs62156221	0.96[EUR][1000 genomes]
rs62156222	0.96[EUR][1000 genomes]
rs62156223	0.98[EUR][1000 genomes]
rs62156228	0.96[EUR][1000 genomes]
rs62156232	0.94[EUR][1000 genomes]
rs6576981	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6576987	1.00[GIH][hapmap]
rs6751132	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6753987	1.00[GIH][hapmap]
rs6758151	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7568206	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7580942	1.00[GIH][hapmap]
rs9948	1.00[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 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
14	nsv874680	chr2:97309574-97678319	Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent Enhancer 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	61 gene(s)	inside rSNPs	diseases
15	nsv834307	chr2:97321447-97479266	Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
16	nsv526313	chr2:97333492-97660619	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription 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 miRNA target site	61 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:97346200-97368000	Weak transcription	Aorta	Aorta
2	chr2:97350400-97367600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:97351800-97368400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr2:97351800-97372800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:97351800-97373600	Weak transcription	Fetal Brain Male	brain
6	chr2:97352000-97368000	Weak transcription	Ovary	ovary
7	chr2:97352000-97368200	Weak transcription	Gastric	stomach
8	chr2:97352200-97367800	Weak transcription	Right Ventricle	heart
9	chr2:97353800-97371200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:97355800-97368400	Weak transcription	NHLF	lung
11	chr2:97356800-97368200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr2:97357600-97366800	Weak transcription	Stomach Smooth Muscle	stomach
13	chr2:97358400-97375400	Weak transcription	Fetal Heart	heart
14	chr2:97358600-97367800	Weak transcription	Brain Anterior Caudate	brain
15	chr2:97358600-97369600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr2:97359200-97368000	Weak transcription	Thymus	Thymus
17	chr2:97360200-97368200	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr2:97360200-97368600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr2:97360600-97367800	Weak transcription	Lung	lung
20	chr2:97360800-97367400	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr2:97360800-97375000	Strong transcription	Fetal Intestine Small	intestine
22	chr2:97360800-97381200	Strong transcription	Fetal Stomach	stomach
23	chr2:97361000-97367800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr2:97361000-97368200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr2:97361000-97370000	Weak transcription	Fetal Lung	lung
26	chr2:97361200-97367400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr2:97361200-97367800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr2:97361200-97370400	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr2:97361200-97370600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr2:97361200-97371600	Weak transcription	Primary hematopoietic stem cells	blood
31	chr2:97361400-97367400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:97361400-97371800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:97361600-97367600	Weak transcription	HepG2	liver
34	chr2:97362000-97367800	Weak transcription	Spleen	Spleen
35	chr2:97362000-97368200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr2:97362200-97368600	Weak transcription	Brain Cingulate Gyrus	brain
37	chr2:97362600-97370000	Weak transcription	Colon Smooth Muscle	Colon
38	chr2:97362600-97376600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr2:97362800-97379800	Strong transcription	Fetal Intestine Large	intestine
40	chr2:97363400-97367400	Weak transcription	Brain Hippocampus Middle	brain
41	chr2:97363800-97367200	Weak transcription	Colonic Mucosa	Colon
42	chr2:97363800-97370600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr2:97364000-97367800	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr2:97364000-97367800	Weak transcription	Liver	Liver
45	chr2:97364200-97370800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr2:97364400-97368200	Weak transcription	Fetal Thymus	thymus
47	chr2:97364600-97367800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr2:97364600-97370000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr2:97364600-97370600	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr2:97364800-97367400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links