Variant report

Variant	rs12616982
Chromosome Location	chr2:55874811-55874812
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr2:55874371-55874899	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:55874598-55875005	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55845275..55847536-chr2:55874365..55876152,2	K562	blood:
2	chr2:55844652..55846516-chr2:55872491..55875236,2	MCF-7	breast:

Variant related genes	Relation type
PNPT1	TF binding region
ENSG00000272606	Chromatin interaction
ENSG00000138041	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10172181	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10172506	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10173150	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10182131	0.94[AMR][1000 genomes]
rs10194634	0.89[AMR][1000 genomes]
rs10195281	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10200159	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10203953	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10204169	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1045920	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10496044	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11676573	0.91[EUR][1000 genomes]
rs11902712	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12615063	0.94[AMR][1000 genomes]
rs12616502	0.91[EUR][1000 genomes]
rs12622830	0.80[EUR][1000 genomes]
rs12623625	0.94[AMR][1000 genomes]
rs13382187	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13383352	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13399762	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13400946	0.94[AMR][1000 genomes]
rs13403782	0.82[AFR][1000 genomes]
rs13407344	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13420929	0.94[AMR][1000 genomes]
rs13428382	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13428486	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13430684	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17047094	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17047119	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2867964	0.94[AMR][1000 genomes]
rs3748955	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6545507	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6545509	1.00[EUR][1000 genomes]
rs6545510	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6545512	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6545513	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6705295	0.89[AMR][1000 genomes]
rs6712314	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6717574	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6725101	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6736996	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6739788	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6760959	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7558127	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7567115	0.94[AMR][1000 genomes]
rs7575906	0.94[AMR][1000 genomes]
rs7582174	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7584120	0.88[AFR][1000 genomes]
rs7586115	0.94[AMR][1000 genomes]
rs7586124	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7586366	0.94[AMR][1000 genomes]
rs7594212	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7594497	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9309267	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9309268	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
3	nsv834080	chr2:55741036-55927928	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
4	esv2757798	chr2:55747239-55981074	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv2759050	chr2:55747239-55981074	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv1008452	chr2:55809191-55987274	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv9791	chr2:55872725-55883751	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55846800-55919800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:55847400-55911000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:55847600-55886600	Weak transcription	Stomach Mucosa	stomach
4	chr2:55849800-55882800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:55853600-55882400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr2:55858200-55920400	Weak transcription	Fetal Heart	heart
7	chr2:55858800-55875600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr2:55858800-55877200	Strong transcription	Dnd41	blood
9	chr2:55859000-55876800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr2:55859000-55877000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:55859000-55877200	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr2:55859400-55875600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:55859400-55877600	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr2:55860400-55905400	Weak transcription	Fetal Brain Male	brain
15	chr2:55861800-55875000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr2:55861800-55875800	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr2:55862000-55875000	Strong transcription	Fetal Intestine Large	intestine
18	chr2:55862000-55877200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr2:55862000-55877800	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr2:55863400-55875600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr2:55864000-55893200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr2:55864200-55882800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr2:55864400-55919600	Weak transcription	NHLF	lung
24	chr2:55864600-55881400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr2:55864600-55881400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr2:55864800-55879200	Weak transcription	Primary hematopoietic stem cells	blood
27	chr2:55865000-55880400	Weak transcription	HMEC	breast
28	chr2:55866200-55882400	Weak transcription	Ovary	ovary
29	chr2:55866600-55920000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr2:55866800-55875000	Strong transcription	Primary T cells fromperipheralblood	blood
31	chr2:55867200-55875000	Strong transcription	H1 Cell Line	embryonic stem cell
32	chr2:55868000-55879200	Weak transcription	NH-A	brain
33	chr2:55870000-55875000	Strong transcription	Primary B cells from cord blood	blood
34	chr2:55870000-55875200	Strong transcription	Placenta	Placenta
35	chr2:55870400-55887600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr2:55870400-55887800	Weak transcription	Fetal Brain Female	brain
37	chr2:55870400-55920000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr2:55870600-55879800	Weak transcription	HUVEC	blood vessel
39	chr2:55870600-55881400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr2:55870600-55892800	Weak transcription	Psoas Muscle	Psoas
41	chr2:55870600-55920000	Weak transcription	Rectal Smooth Muscle	rectum
42	chr2:55870800-55879200	Weak transcription	Brain Hippocampus Middle	brain
43	chr2:55870800-55888000	Weak transcription	Colonic Mucosa	Colon
44	chr2:55870800-55893400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr2:55870800-55903600	Weak transcription	Gastric	stomach
46	chr2:55870800-55909000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr2:55870800-55920400	Weak transcription	Aorta	Aorta
48	chr2:55871000-55879000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr2:55871000-55880000	Weak transcription	Right Ventricle	heart
50	chr2:55871000-55880600	Weak transcription	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links