Variant report

Variant	rs12996029
Chromosome Location	chr2:38819906-38819907
allele	A/G
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:11)
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	POLR2A	chr2:38819159-38821053	K562	blood:	n/a	n/a
2	CEBPB	chr2:38819768-38820049	K562	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:38816751..38822030-chr2:38827238..38830922,5	MCF-7	breast:
2	chr2:38301826..38303354-chr2:38817276..38820176,2	MCF-7	breast:
3	chr2:38819178..38822144-chr2:38914195..38916450,2	K562	blood:
4	chr2:38819202..38822030-chr2:38909046..38911240,2	K562	blood:
5	chr2:38816358..38820230-chr2:38976960..38979820,4	MCF-7	breast:
6	chr2:38819128..38833161-chr2:38974716..38980003,37	K562	blood:
7	chr2:38816590..38821819-chr2:38825503..38830021,9	MCF-7	breast:
8	chr2:38764122..38766305-chr2:38818986..38821138,2	K562	blood:
9	chr2:38818005..38820191-chr2:38893287..38895221,2	K562	blood:
10	chr2:38816516..38836019-chr2:38963690..38980163,62	K562	blood:
11	chr2:38778255..38779937-chr2:38819083..38821616,2	K562	blood:

No data

Variant related genes	Relation type
HNRNPLL	TF binding region
ENSG00000232973	Chromatin interaction
ENSG00000138061	Chromatin interaction
ENSG00000143889	Chromatin interaction
ENSG00000143891	Chromatin interaction
ENSG00000152147	Chromatin interaction
ENSG00000115875	Chromatin interaction
ENSG00000235586	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10204680	0.83[CHD][hapmap];0.82[MEX][hapmap]
rs10495880	0.89[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12987111	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12990659	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12991911	0.94[CEU][hapmap];0.97[EUR][1000 genomes]
rs12995222	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13011896	0.87[AFR][1000 genomes]
rs13431551	0.83[EUR][1000 genomes]
rs1368114	0.83[EUR][1000 genomes]
rs1540436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17421378	0.94[CEU][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.83[EUR][1000 genomes]
rs17421399	0.90[JPT][hapmap];1.00[YRI][hapmap]
rs17421503	1.00[ASW][hapmap];0.94[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17421545	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17421587	0.84[EUR][1000 genomes]
rs17421743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17493321	0.90[JPT][hapmap];0.81[YRI][hapmap]
rs17493363	0.87[CEU][hapmap];0.81[YRI][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17493370	0.89[ASW][hapmap];0.80[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17493419	0.94[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17493538	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]
rs17493573	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17493594	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs17493839	0.84[ASN][1000 genomes]
rs17575960	0.81[CEU][hapmap]
rs17603796	0.80[ASN][1000 genomes]
rs1864828	1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1864829	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1864830	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2253519	0.82[EUR][1000 genomes]
rs3213851	0.81[ASN][1000 genomes]
rs34462852	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34533895	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34688430	0.88[ASN][1000 genomes]
rs34821677	0.88[ASN][1000 genomes]
rs35151237	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35219064	0.99[EUR][1000 genomes]
rs35378647	0.88[ASN][1000 genomes]
rs35492507	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35581112	0.91[ASN][1000 genomes]
rs35679136	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35734673	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35869291	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4268910	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4536633	0.88[ASN][1000 genomes]
rs55948796	0.88[ASN][1000 genomes]
rs56208611	0.89[ASN][1000 genomes]
rs56217714	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6544169	0.82[EUR][1000 genomes]
rs6544170	0.91[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap]
rs6704829	0.89[ASN][1000 genomes]
rs6710118	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6722560	0.88[ASN][1000 genomes]
rs6731029	1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs6733848	1.00[CHB][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap];0.86[TSI][hapmap];0.89[ASN][1000 genomes]
rs6736320	0.82[EUR][1000 genomes]
rs6745023	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6749343	0.90[EUR][1000 genomes]
rs6750764	0.88[ASN][1000 genomes]
rs68109027	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72795154	0.81[EUR][1000 genomes]
rs72905846	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72905865	0.80[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs72907903	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7573095	0.83[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs7574556	0.90[JPT][hapmap];0.82[YRI][hapmap]
rs891705	0.89[JPT][hapmap]
rs919698	0.88[CEU][hapmap]
rs934394	0.93[CEU][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs934395	0.94[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][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:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38775800-38821800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:38779400-38821800	Weak transcription	Right Ventricle	heart
3	chr2:38781200-38827600	Weak transcription	Esophagus	oesophagus
4	chr2:38783800-38827800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:38785000-38827600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:38786000-38827600	Weak transcription	Colonic Mucosa	Colon
7	chr2:38798000-38827600	Weak transcription	Spleen	Spleen
8	chr2:38798200-38820600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr2:38798200-38821800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr2:38798200-38827600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr2:38798800-38822000	Weak transcription	NHEK	skin
12	chr2:38799800-38827800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr2:38805200-38826400	Weak transcription	Primary hematopoietic stem cells	blood
14	chr2:38808200-38824400	Weak transcription	Hela-S3	cervix
15	chr2:38808400-38820400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr2:38808800-38821800	Weak transcription	HMEC	breast
17	chr2:38808800-38825200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr2:38808800-38825400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr2:38808800-38827000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr2:38808800-38827400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr2:38808800-38827400	Weak transcription	Pancreas	Pancrea
22	chr2:38809000-38824200	Weak transcription	Liver	Liver
23	chr2:38809000-38825600	Weak transcription	Brain Cingulate Gyrus	brain
24	chr2:38809400-38825800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr2:38809600-38827400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr2:38810000-38827600	Weak transcription	Fetal Muscle Trunk	muscle
27	chr2:38812600-38823800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr2:38813000-38821800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr2:38813000-38821800	Weak transcription	Adipose Nuclei	Adipose
30	chr2:38813000-38823800	Weak transcription	Duodenum Mucosa	Duodenum
31	chr2:38813200-38826000	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr2:38813400-38827000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr2:38813800-38825400	Weak transcription	Primary T cells from cord blood	blood
34	chr2:38814400-38825200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr2:38814400-38825600	Weak transcription	HUVEC	blood vessel
36	chr2:38814600-38824200	Weak transcription	Fetal Brain Female	brain
37	chr2:38815200-38824000	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr2:38815200-38824000	Weak transcription	Fetal Intestine Large	intestine
39	chr2:38815200-38825200	Weak transcription	Gastric	stomach
40	chr2:38815200-38825400	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr2:38815200-38825800	Weak transcription	Fetal Brain Male	brain
42	chr2:38815400-38820200	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr2:38815400-38824200	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr2:38815400-38825400	Weak transcription	Fetal Kidney	kidney
45	chr2:38815600-38821800	Weak transcription	Lung	lung
46	chr2:38816800-38821800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr2:38817200-38820200	Weak transcription	Brain Anterior Caudate	brain
48	chr2:38817400-38820600	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr2:38817400-38824000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr2:38817600-38824200	Weak transcription	HUES64 Cell Line	embryonic stem cell

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