Variant report

Variant	rs833843
Chromosome Location	chr12:49364391-49364392
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	CTBP2	chr12:49362803-49365797	H1-hESC	embryonic stem cell:	n/a	n/a
2	SUZ12	chr12:49363798-49366856	H1-hESC	embryonic stem cell:	n/a	n/a
3	MAX	chr12:49364367-49365979	A549	lung:	n/a	chr12:49364858-49364868 chr12:49365173-49365183
4	MAX	chr12:49363624-49364428	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:49351084..49352752-chr12:49363357..49365742,2	K562	blood:
2	chr12:49363715..49365253-chr12:49387524..49389322,2	MCF-7	breast:
3	chr12:49318968..49320565-chr12:49363213..49364979,2	MCF-7	breast:
4	chr12:49348867..49353149-chr12:49362475..49369316,15	MCF-7	breast:
5	chr12:49347357..49351835-chr12:49360389..49366684,9	MCF-7	breast:

Variant related genes	Relation type
RNU6-940P	TF binding region
ENSG00000134285	Chromatin interaction
ENSG00000272822	Chromatin interaction
ENSG00000258283	Chromatin interaction
ENSG00000134287	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1051886	0.86[CHB][hapmap];0.91[CHD][hapmap];0.86[ASN][1000 genomes]
rs1054376	0.89[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs10747556	0.82[CHB][hapmap];0.88[CHD][hapmap];0.81[JPT][hapmap]
rs10747557	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs10747558	0.84[CHB][hapmap];0.85[ASN][1000 genomes]
rs10783289	0.86[CHB][hapmap];0.89[CHD][hapmap]
rs10783293	0.86[CHB][hapmap];0.85[CHD][hapmap];0.80[ASN][1000 genomes]
rs10783294	0.86[CHB][hapmap];0.86[CHD][hapmap];0.80[ASN][1000 genomes]
rs10783295	0.80[ASN][1000 genomes]
rs10783297	0.84[ASN][1000 genomes]
rs10875883	0.85[CEU][hapmap];0.87[MEX][hapmap]
rs10875886	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs10875893	0.86[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap]
rs10875894	0.86[CHB][hapmap];0.86[CHD][hapmap];0.80[ASN][1000 genomes]
rs10875895	0.80[ASN][1000 genomes]
rs10875897	0.82[CHB][hapmap];0.86[CHD][hapmap];0.84[ASN][1000 genomes]
rs10875898	0.81[CHB][hapmap];0.84[ASN][1000 genomes]
rs10875900	0.86[ASN][1000 genomes]
rs10875901	0.85[ASN][1000 genomes]
rs10875902	0.82[CHB][hapmap];0.91[CHD][hapmap];0.86[ASN][1000 genomes]
rs1111662	0.86[CHB][hapmap];0.86[CHD][hapmap];0.83[MEX][hapmap];0.85[ASN][1000 genomes]
rs11168783	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs11168784	0.86[CHB][hapmap]
rs11168785	0.86[CHB][hapmap];0.84[CHD][hapmap];0.80[ASN][1000 genomes]
rs11168790	0.86[CHB][hapmap];0.86[CHD][hapmap];0.80[ASN][1000 genomes]
rs11168792	0.82[ASN][1000 genomes]
rs11168794	0.82[ASN][1000 genomes]
rs11168795	0.85[ASN][1000 genomes]
rs11168797	0.85[ASN][1000 genomes]
rs11168803	0.86[ASN][1000 genomes]
rs11168811	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11168812	0.86[ASN][1000 genomes]
rs11608916	0.81[ASN][1000 genomes]
rs11610459	0.80[ASN][1000 genomes]
rs11610497	0.80[ASN][1000 genomes]
rs11614474	0.80[ASN][1000 genomes]
rs12229275	0.80[ASN][1000 genomes]
rs12423542	0.86[CHB][hapmap];0.86[CHD][hapmap];0.82[ASN][1000 genomes]
rs12579249	0.80[ASN][1000 genomes]
rs1690182	0.86[ASN][1000 genomes]
rs1818996	0.84[ASN][1000 genomes]
rs1830192	0.82[CHB][hapmap];0.84[ASN][1000 genomes]
rs2030900	0.82[CHB][hapmap];0.85[ASN][1000 genomes]
rs2070940	0.82[CHB][hapmap];0.85[ASN][1000 genomes]
rs2073480	0.86[CHB][hapmap];0.86[CHD][hapmap];0.85[ASN][1000 genomes]
rs2131713	0.81[CHB][hapmap];0.84[ASN][1000 genomes]
rs2272311	0.82[CHB][hapmap];0.86[CHD][hapmap];0.83[ASN][1000 genomes]
rs2272312	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs2293449	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs2453063	0.86[ASN][1000 genomes]
rs2463175	0.85[ASN][1000 genomes]
rs2641450	0.83[ASN][1000 genomes]
rs2694839	0.85[ASN][1000 genomes]
rs2694840	0.83[ASN][1000 genomes]
rs3741627	0.86[CHB][hapmap];0.91[CHD][hapmap];0.86[ASN][1000 genomes]
rs3759146	0.86[CHB][hapmap];0.86[CHD][hapmap];0.81[ASN][1000 genomes]
rs3782353	0.86[CHB][hapmap];0.91[CHD][hapmap];0.86[ASN][1000 genomes]
rs3809147	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs3825182	0.86[CHB][hapmap];0.86[CHD][hapmap];0.81[ASN][1000 genomes]
rs3825184	0.86[CHB][hapmap];0.86[CHD][hapmap];0.83[MEX][hapmap]
rs4018510	0.84[ASN][1000 genomes]
rs4237854	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs4433614	0.86[CHB][hapmap]
rs4526804	0.85[ASN][1000 genomes]
rs4760600	0.86[CHB][hapmap];0.86[CHD][hapmap]
rs4760661	0.81[ASN][1000 genomes]
rs4760662	0.91[CHB][hapmap];0.91[CHD][hapmap];0.86[ASN][1000 genomes]
rs4760663	0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[ASN][1000 genomes]
rs4760664	0.85[ASN][1000 genomes]
rs4760666	0.86[CHB][hapmap];0.86[CHD][hapmap];0.83[ASN][1000 genomes]
rs4760667	0.81[CHB][hapmap];0.84[ASN][1000 genomes]
rs4760668	0.86[ASN][1000 genomes]
rs58023472	0.80[ASN][1000 genomes]
rs59087236	0.85[ASN][1000 genomes]
rs61942166	0.84[ASN][1000 genomes]
rs61942167	0.85[ASN][1000 genomes]
rs61942169	0.86[ASN][1000 genomes]
rs61942207	0.85[ASN][1000 genomes]
rs61942209	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6580696	0.86[CHB][hapmap];0.86[CHD][hapmap];0.86[ASN][1000 genomes]
rs7297958	0.85[CHB][hapmap];0.88[CHD][hapmap];0.80[ASN][1000 genomes]
rs7298330	0.80[ASN][1000 genomes]
rs7304942	0.80[ASN][1000 genomes]
rs7313988	0.85[ASN][1000 genomes]
rs7963018	0.86[ASN][1000 genomes]
rs7963160	0.86[ASN][1000 genomes]
rs7976473	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs833476	0.85[CEU][hapmap]
rs833820	0.96[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs833821	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs833822	0.82[CHB][hapmap];0.86[CHD][hapmap];0.83[MEX][hapmap];0.85[ASN][1000 genomes]
rs833827	0.85[ASN][1000 genomes]
rs833828	0.83[ASN][1000 genomes]
rs833839	0.94[ASN][1000 genomes]
rs833840	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs833841	1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.95[ASN][1000 genomes]
rs833842	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9783452	0.82[CHB][hapmap];0.86[CHD][hapmap];0.85[ASN][1000 genomes]
rs9783477	0.85[ASN][1000 genomes]
rs9788029	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9796008	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832404	chr12:49258560-49458555	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
4	nsv558833	chr12:49358880-49478812	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs833843	FKBP11	cis	cerebellum	SCAN
rs833843	AQP2	cis	parietal	SCAN
rs833843	PRPH	cis	parietal	SCAN
rs833843	CCDC65	cis	Esophagus Muscularis	GTEx
rs833843	FKBP11	cis	parietal	SCAN
rs833843	ADCY6	cis	parietal	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49351800-49365000	Weak transcription	Right Atrium	heart
2	chr12:49362600-49364600	Enhancers	A549	lung
3	chr12:49362800-49365000	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr12:49362800-49365200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
5	chr12:49362800-49366000	Bivalent Enhancer	Fetal Intestine Large	intestine
6	chr12:49363000-49364400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr12:49363000-49364400	Enhancers	Lung	lung
8	chr12:49363000-49364800	Enhancers	HMEC	breast
9	chr12:49363000-49365200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
10	chr12:49363000-49365200	Bivalent Enhancer	Fetal Intestine Small	intestine
11	chr12:49363000-49365200	Bivalent Enhancer	Placenta	Placenta
12	chr12:49363000-49366000	Enhancers	Pancreas	Pancrea
13	chr12:49363200-49364400	Weak transcription	Hela-S3	cervix
14	chr12:49363200-49365000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:49363200-49365200	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
16	chr12:49363200-49365800	Bivalent Enhancer	Primary B cells from cord blood	blood
17	chr12:49363200-49366200	Bivalent Enhancer	Stomach Mucosa	stomach
18	chr12:49363400-49364400	Bivalent Enhancer	Fetal Brain Male	brain
19	chr12:49363400-49364800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
20	chr12:49363400-49364800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
21	chr12:49363400-49364800	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum
22	chr12:49363400-49365000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr12:49363400-49365000	Bivalent Enhancer	Primary hematopoietic stem cells	blood
24	chr12:49363400-49365200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
25	chr12:49363400-49366200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
26	chr12:49363600-49364400	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr12:49363600-49364400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
28	chr12:49363600-49364400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr12:49363600-49364600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
30	chr12:49363600-49364600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
31	chr12:49363600-49365000	Flanking Bivalent TSS/Enh	HepG2	liver
32	chr12:49363600-49365000	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
33	chr12:49363600-49366000	Bivalent Enhancer	Fetal Heart	heart
34	chr12:49363600-49368000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
35	chr12:49363800-49364400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr12:49363800-49364400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr12:49363800-49364400	Bivalent Enhancer	Left Ventricle	heart
38	chr12:49363800-49364400	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
39	chr12:49363800-49364400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
40	chr12:49363800-49364600	Bivalent/Poised TSS	Brain Angular Gyrus	brain
41	chr12:49363800-49364600	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
42	chr12:49363800-49364600	Flanking Bivalent TSS/Enh	Thymus	Thymus
43	chr12:49363800-49364800	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
44	chr12:49363800-49365200	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
45	chr12:49363800-49365400	Bivalent Enhancer	Fetal Stomach	stomach
46	chr12:49363800-49365400	Flanking Active TSS	Placenta Amnion	Placenta Amnion
47	chr12:49363800-49365800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr12:49363800-49366200	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
49	chr12:49364000-49364400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
50	chr12:49364000-49364400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell

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