Variant report

Variant	rs17493538
Chromosome Location	chr2:38806329-38806330
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:38803779..38806486-chr2:38953077..38954678,2	MCF-7	breast:
2	chr2:38806174..38811270-chr2:38966687..38973672,10	K562	blood:
3	chr2:38805174..38810149-chr2:38974397..38979817,14	K562	blood:
4	chr2:38802059..38810352-chr2:38974835..38979723,14	K562	blood:
5	chr2:38806069..38807840-chr2:38828104..38829708,2	MCF-7	breast:
6	chr2:38749021..38751091-chr2:38805998..38807763,2	K562	blood:
7	chr2:38600866..38603668-chr2:38806016..38808149,2	K562	blood:
8	chr2:38788831..38791185-chr2:38805225..38808104,2	K562	blood:
9	chr2:38805084..38807176-chr2:38944983..38947545,2	K562	blood:
10	chr2:38805850..38810073-chr2:38814750..38818900,5	MCF-7	breast:
11	chr2:38806248..38808565-chr2:38954475..38956582,2	K562	blood:
12	chr2:38800010..38801943-chr2:38804544..38806544,2	MCF-7	breast:
13	chr2:38805216..38808046-chr2:38947623..38949999,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000115875	Chromatin interaction
ENSG00000143889	Chromatin interaction
ENSG00000119787	Chromatin interaction
ENSG00000152147	Chromatin interaction
ENSG00000235586	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10204680	0.89[MEX][hapmap]
rs10495880	0.81[ASW][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.84[ASN][1000 genomes]
rs12105827	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12987111	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs12990659	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12995222	0.83[ASN][1000 genomes]
rs12996029	0.90[ASW][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.89[MEX][hapmap];0.85[MKK][hapmap];0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs1540436	1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[ASN][1000 genomes]
rs17421378	0.90[JPT][hapmap];0.94[YRI][hapmap]
rs17421399	1.00[CEU][hapmap];0.90[JPT][hapmap];0.90[EUR][1000 genomes]
rs17421503	0.90[ASW][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap]
rs17421743	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17493321	0.94[CEU][hapmap];0.90[JPT][hapmap];0.94[YRI][hapmap];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17493363	0.94[YRI][hapmap];0.80[AFR][1000 genomes]
rs17493370	1.00[ASW][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes]
rs17493419	0.90[JPT][hapmap]
rs17493573	1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs17493594	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1864828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1864829	0.83[ASN][1000 genomes]
rs1864830	0.83[ASN][1000 genomes]
rs3213851	0.98[ASN][1000 genomes]
rs34218951	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34462852	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs35734673	0.81[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs35933789	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3731843	0.81[CHD][hapmap]
rs4268910	0.90[ASW][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[TSI][hapmap];0.88[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs56217714	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6544170	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6721860	0.84[EUR][1000 genomes]
rs6731029	0.89[JPT][hapmap]
rs6733848	0.89[JPT][hapmap]
rs6745023	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6757844	0.82[EUR][1000 genomes]
rs72905865	0.84[ASN][1000 genomes]
rs72907903	0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7573095	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7574556	1.00[CEU][hapmap];0.90[JPT][hapmap];0.94[YRI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs891705	0.89[JPT][hapmap]
rs934394	0.89[JPT][hapmap];0.93[YRI][hapmap]
rs934395	0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers 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	141 gene(s)	inside rSNPs	diseases
3	nsv873881	chr2:38745624-38877636	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv581482	chr2:38799820-38858669	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv581483	chr2:38799820-38862223	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv581484	chr2:38799820-38874177	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38763600-38809600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:38768200-38812800	Weak transcription	Psoas Muscle	Psoas
3	chr2:38775800-38821800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:38777000-38807200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr2:38779000-38818200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:38779400-38821800	Weak transcription	Right Ventricle	heart
7	chr2:38779600-38807400	Weak transcription	Fetal Heart	heart
8	chr2:38779600-38812800	Weak transcription	Aorta	Aorta
9	chr2:38781200-38827600	Weak transcription	Esophagus	oesophagus
10	chr2:38782400-38819000	Strong transcription	Fetal Thymus	thymus
11	chr2:38783800-38827800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:38785000-38827600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:38786000-38827600	Weak transcription	Colonic Mucosa	Colon
14	chr2:38786400-38818800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:38786600-38819000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr2:38787200-38807000	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr2:38787200-38807000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr2:38787400-38806400	Strong transcription	Dnd41	blood
19	chr2:38790800-38807000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr2:38792600-38810200	Strong transcription	K562	blood
21	chr2:38795200-38807200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr2:38795200-38808400	Weak transcription	Left Ventricle	heart
23	chr2:38795200-38808400	Weak transcription	Lung	lung
24	chr2:38795200-38808400	Weak transcription	Ovary	ovary
25	chr2:38795200-38809200	Weak transcription	Fetal Intestine Small	intestine
26	chr2:38795200-38809200	Weak transcription	Fetal Stomach	stomach
27	chr2:38795200-38814800	Weak transcription	Gastric	stomach
28	chr2:38795400-38808200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr2:38795600-38808400	Weak transcription	Brain Cingulate Gyrus	brain
30	chr2:38796200-38808200	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr2:38796400-38808400	Weak transcription	Brain Angular Gyrus	brain
32	chr2:38796400-38812800	Weak transcription	Small Intestine	intestine
33	chr2:38796600-38808600	Weak transcription	Brain Hippocampus Middle	brain
34	chr2:38798000-38808000	Weak transcription	Colon Smooth Muscle	Colon
35	chr2:38798000-38818000	Weak transcription	Stomach Mucosa	stomach
36	chr2:38798000-38827600	Weak transcription	Spleen	Spleen
37	chr2:38798200-38808000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr2:38798200-38808400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr2:38798200-38808400	Weak transcription	Pancreas	Pancrea
40	chr2:38798200-38812800	Weak transcription	Fetal Muscle Leg	muscle
41	chr2:38798200-38812800	Weak transcription	Thymus	Thymus
42	chr2:38798200-38820600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr2:38798200-38821800	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr2:38798200-38827600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr2:38798600-38808000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr2:38798600-38808000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr2:38798600-38808200	Weak transcription	Stomach Smooth Muscle	stomach
48	chr2:38798600-38816400	Weak transcription	Brain Germinal Matrix	brain
49	chr2:38798800-38808200	Weak transcription	Fetal Brain Female	brain
50	chr2:38798800-38817000	Weak transcription	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links