Variant report

Variant	rs72905880
Chromosome Location	chr2:38800877-38800878
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

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

No data

(count:7 , 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	chr2:38799758..38802428-chr2:38829312..38831287,2	MCF-7	breast:
4	chr2:38798201..38801159-chr2:38970584..38973255,2	K562	blood:
5	chr2:38795602..38798483-chr2:38799453..38802179,2	MCF-7	breast:
6	chr2:38798820..38803469-chr2:38977368..38979935,4	MCF-7	breast:
7	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: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1543880	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17022945	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs41446253	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55773228	0.92[AFR][1000 genomes]
rs55785223	0.87[AMR][1000 genomes]
rs55820712	0.84[AFR][1000 genomes]
rs55833813	0.87[AMR][1000 genomes]
rs55957936	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56251362	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56956410	0.87[AMR][1000 genomes]
rs59114683	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60475078	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6727765	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6732384	0.85[AMR][1000 genomes]
rs6732743	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72895897	0.87[AMR][1000 genomes]
rs72897608	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72897610	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72905837	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72905839	0.87[AMR][1000 genomes]
rs72905843	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72905844	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72905847	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72905860	0.88[AFR][1000 genomes]
rs72905861	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72905863	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72905868	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72905869	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72905871	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72907906	0.81[AFR][1000 genomes]
rs73929040	0.87[AMR][1000 genomes]
rs73929050	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73929059	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs73929077	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73931606	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7579589	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7594264	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes]

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	chr2:38785400-38801400	Weak transcription	GM12878-XiMat	blood
14	chr2:38786000-38827600	Weak transcription	Colonic Mucosa	Colon
15	chr2:38786400-38806200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr2:38786400-38818800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:38786600-38819000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:38787200-38802800	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr2:38787200-38805600	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr2:38787200-38806200	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr2:38787200-38807000	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr2:38787200-38807000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr2:38787400-38802400	Strong transcription	HepG2	liver
24	chr2:38787400-38804400	Strong transcription	Placenta	Placenta
25	chr2:38787400-38806400	Strong transcription	Dnd41	blood
26	chr2:38790800-38807000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr2:38791200-38801800	Strong transcription	Duodenum Mucosa	Duodenum
28	chr2:38791200-38802200	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr2:38791200-38805200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr2:38791400-38801800	Strong transcription	Primary T helper cells fromperipheralblood	blood
31	chr2:38792600-38801200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr2:38792600-38810200	Strong transcription	K562	blood
33	chr2:38793000-38802200	Strong transcription	Adipose Nuclei	Adipose
34	chr2:38794600-38801800	Strong transcription	HUVEC	blood vessel
35	chr2:38795200-38807200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr2:38795200-38808400	Weak transcription	Left Ventricle	heart
37	chr2:38795200-38808400	Weak transcription	Lung	lung
38	chr2:38795200-38808400	Weak transcription	Ovary	ovary
39	chr2:38795200-38809200	Weak transcription	Fetal Intestine Small	intestine
40	chr2:38795200-38809200	Weak transcription	Fetal Stomach	stomach
41	chr2:38795200-38814800	Weak transcription	Gastric	stomach
42	chr2:38795400-38808200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr2:38795600-38804400	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr2:38795600-38808400	Weak transcription	Brain Cingulate Gyrus	brain
45	chr2:38796200-38808200	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr2:38796400-38804200	Weak transcription	Fetal Brain Male	brain
47	chr2:38796400-38808400	Weak transcription	Brain Angular Gyrus	brain
48	chr2:38796400-38812800	Weak transcription	Small Intestine	intestine
49	chr2:38796600-38808600	Weak transcription	Brain Hippocampus Middle	brain
50	chr2:38797000-38806000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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