Variant report

Variant	rs12991911
Chromosome Location	chr2:38801460-38801461
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FAM48A	chr2:38801450-38801559	GM12878	blood:	n/a	n/a
2	POLR2A	chr2:38793541-38809540	K562	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:38800582..38805538-chr2:38967531..38972325,7	K562	blood:
2	chr2:38800010..38801943-chr2:38804544..38806544,2	MCF-7	breast:
3	chr2:38801102..38805914-chr2:38807147..38811065,7	MCF-7	breast:
4	chr2:38792540..38795008-chr2:38800997..38802602,2	MCF-7	breast:
5	chr2:38801114..38803068-chr2:38977884..38979535,2	MCF-7	breast:
6	chr2:38799758..38802428-chr2:38829312..38831287,2	MCF-7	breast:
7	chr2:38795602..38798483-chr2:38799453..38802179,2	MCF-7	breast:
8	chr2:38798820..38803469-chr2:38977368..38979935,4	MCF-7	breast:
9	chr2:38799759..38801518-chr2:38974741..38978178,3	K562	blood:

No data

Variant related genes	Relation type
HNRNPLL	TF binding region
ENSG00000143889	Chromatin interaction
ENSG00000115875	Chromatin interaction
ENSG00000152147	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10204680	0.83[CEU][hapmap]
rs10495880	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs11890666	1.00[ASN][1000 genomes]
rs12987111	0.96[EUR][1000 genomes]
rs12990659	0.96[EUR][1000 genomes]
rs12995222	0.97[EUR][1000 genomes]
rs12996029	0.94[CEU][hapmap];0.97[EUR][1000 genomes]
rs13431551	0.80[EUR][1000 genomes]
rs1368114	0.80[EUR][1000 genomes]
rs1540436	0.88[CEU][hapmap];0.95[EUR][1000 genomes]
rs17421378	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs17421503	0.87[CEU][hapmap]
rs17421587	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17421743	0.89[CEU][hapmap];0.94[EUR][1000 genomes]
rs17493363	0.88[CEU][hapmap]
rs17493370	0.86[CEU][hapmap]
rs17493419	0.83[CEU][hapmap]
rs17493573	0.94[CEU][hapmap];0.96[EUR][1000 genomes]
rs17575960	0.83[CEU][hapmap]
rs1864829	0.91[EUR][1000 genomes]
rs1864830	0.94[EUR][1000 genomes]
rs34462852	0.97[EUR][1000 genomes]
rs34533895	0.94[EUR][1000 genomes]
rs35151237	0.81[EUR][1000 genomes]
rs35219064	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35492507	0.86[EUR][1000 genomes]
rs35679136	0.83[EUR][1000 genomes]
rs35734673	0.97[EUR][1000 genomes]
rs35869291	0.81[EUR][1000 genomes]
rs4268910	0.94[CEU][hapmap];0.96[EUR][1000 genomes]
rs6710118	0.89[EUR][1000 genomes]
rs6742843	0.82[CEU][hapmap]
rs6749343	0.88[EUR][1000 genomes]
rs72795151	1.00[ASN][1000 genomes]
rs72795154	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72907903	0.97[EUR][1000 genomes]
rs934394	0.82[CEU][hapmap]
rs934395	0.83[CEU][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:121 , 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	chr2:38786400-38806200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr2:38786400-38818800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:38786600-38819000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr2:38787200-38802800	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr2:38787200-38805600	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr2:38787200-38806200	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr2:38787200-38807000	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr2:38787200-38807000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
22	chr2:38787400-38802400	Strong transcription	HepG2	liver
23	chr2:38787400-38804400	Strong transcription	Placenta	Placenta
24	chr2:38787400-38806400	Strong transcription	Dnd41	blood
25	chr2:38790800-38807000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr2:38791200-38801800	Strong transcription	Duodenum Mucosa	Duodenum
27	chr2:38791200-38802200	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr2:38791200-38805200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr2:38791400-38801800	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr2:38792600-38810200	Strong transcription	K562	blood
31	chr2:38793000-38802200	Strong transcription	Adipose Nuclei	Adipose
32	chr2:38794600-38801800	Strong transcription	HUVEC	blood vessel
33	chr2:38795200-38807200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr2:38795200-38808400	Weak transcription	Left Ventricle	heart
35	chr2:38795200-38808400	Weak transcription	Lung	lung
36	chr2:38795200-38808400	Weak transcription	Ovary	ovary
37	chr2:38795200-38809200	Weak transcription	Fetal Intestine Small	intestine
38	chr2:38795200-38809200	Weak transcription	Fetal Stomach	stomach
39	chr2:38795200-38814800	Weak transcription	Gastric	stomach
40	chr2:38795400-38808200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr2:38795600-38804400	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr2:38795600-38808400	Weak transcription	Brain Cingulate Gyrus	brain
43	chr2:38796200-38808200	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr2:38796400-38804200	Weak transcription	Fetal Brain Male	brain
45	chr2:38796400-38808400	Weak transcription	Brain Angular Gyrus	brain
46	chr2:38796400-38812800	Weak transcription	Small Intestine	intestine
47	chr2:38796600-38808600	Weak transcription	Brain Hippocampus Middle	brain
48	chr2:38797000-38806000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr2:38798000-38808000	Weak transcription	Colon Smooth Muscle	Colon
50	chr2:38798000-38818000	Weak transcription	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links