Variant report

Variant	rs833840
Chromosome Location	chr12:49366150-49366151
allele	C/G
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	SUZ12	chr12:49363798-49366856	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr12:49364845-49367135	NB4	blood:	n/a	chr12:49364858-49364868 chr12:49365173-49365183 chr12:49366530-49366539
3	ZNF263	chr12:49364568-49366429	HEK293-T-REx	kidney:	n/a	chr12:49365412-49365433 chr12:49364910-49364919 chr12:49364753-49364762 chr12:49365612-49365621
4	MYC	chr12:49364997-49366825	NB4	blood:	n/a	chr12:49365173-49365183 chr12:49366530-49366539

No.	Distal block	Cell Line	Cell type
1	chr12:49365653..49367190-chr12:49391063..49393227,2	K562	blood:
2	chr12:49348867..49353149-chr12:49362475..49369316,15	MCF-7	breast:
3	chr12:49347357..49351835-chr12:49360389..49366684,9	MCF-7	breast:
4	chr12:49365267..49367565-chr12:49453514..49456197,2	K562	blood:
5	chr12:49365293..49369225-chr12:49386844..49389863,3	MCF-7	breast:
6	chr12:49365791..49367365-chr12:49376844..49379494,2	MCF-7	breast:

Variant related genes	Relation type
RNU6-940P	TF binding region
WNT10B	TF binding region
ENSG00000181418	Chromatin interaction
ENSG00000272822	Chromatin interaction
ENSG00000257913	Chromatin interaction
ENSG00000167548	Chromatin interaction
ENSG00000258283	Chromatin interaction
ENSG00000134287	Chromatin interaction

Extended variants
information (count: 120 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:116)

rs_ID	r²[population]
rs1051886	0.86[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs1054376	0.89[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs10747556	0.82[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs10747557	0.90[CHB][hapmap];0.88[ASN][1000 genomes]
rs10747558	0.84[CHB][hapmap];0.89[ASN][1000 genomes]
rs10783289	0.86[CHB][hapmap];0.89[CHD][hapmap];0.83[ASN][1000 genomes]
rs10783293	0.86[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs10783294	0.86[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs10783295	0.84[ASN][1000 genomes]
rs10783297	0.88[ASN][1000 genomes]
rs10875883	0.85[CEU][hapmap];0.82[MEX][hapmap]
rs10875886	0.86[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs10875893	0.86[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs10875894	0.86[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs10875895	0.84[ASN][1000 genomes]
rs10875896	0.81[ASN][1000 genomes]
rs10875897	0.82[CHB][hapmap];0.86[CHD][hapmap];0.88[ASN][1000 genomes]
rs10875898	0.81[CHB][hapmap];0.88[ASN][1000 genomes]
rs10875899	0.82[ASN][1000 genomes]
rs10875900	0.90[ASN][1000 genomes]
rs10875901	0.89[ASN][1000 genomes]
rs10875902	0.82[CHB][hapmap];0.91[CHD][hapmap];0.88[ASN][1000 genomes]
rs1111662	0.86[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs11168779	0.83[ASN][1000 genomes]
rs11168783	0.86[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs11168784	0.86[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs11168785	0.86[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs11168790	0.86[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs11168792	0.86[ASN][1000 genomes]
rs11168794	0.86[ASN][1000 genomes]
rs11168795	0.88[ASN][1000 genomes]
rs11168797	0.88[ASN][1000 genomes]
rs11168798	0.84[ASN][1000 genomes]
rs11168800	0.84[ASN][1000 genomes]
rs11168801	0.84[ASN][1000 genomes]
rs11168803	0.90[ASN][1000 genomes]
rs11168811	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11168812	0.90[ASN][1000 genomes]
rs11608916	0.84[ASN][1000 genomes]
rs11610459	0.84[ASN][1000 genomes]
rs11610497	0.84[ASN][1000 genomes]
rs11614474	0.84[ASN][1000 genomes]
rs12227240	0.81[ASN][1000 genomes]
rs12228521	0.83[ASN][1000 genomes]
rs12229275	0.84[ASN][1000 genomes]
rs12423542	0.86[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs12579249	0.84[ASN][1000 genomes]
rs1318692	0.83[ASN][1000 genomes]
rs1690182	0.88[ASN][1000 genomes]
rs1818996	0.88[ASN][1000 genomes]
rs1830192	0.82[CHB][hapmap];0.88[ASN][1000 genomes]
rs2030900	0.82[CHB][hapmap];0.88[ASN][1000 genomes]
rs2070940	0.82[CHB][hapmap];0.88[ASN][1000 genomes]
rs2073480	0.86[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs2131713	0.81[CHB][hapmap];0.83[JPT][hapmap];0.88[ASN][1000 genomes]
rs2272311	0.82[CHB][hapmap];0.86[CHD][hapmap];0.87[ASN][1000 genomes]
rs2272312	0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs2293449	0.86[CHB][hapmap];0.86[ASN][1000 genomes]
rs2368701	0.83[ASN][1000 genomes]
rs2453063	0.90[ASN][1000 genomes]
rs2463175	0.89[ASN][1000 genomes]
rs2641450	0.86[ASN][1000 genomes]
rs2694839	0.88[ASN][1000 genomes]
rs2694840	0.87[ASN][1000 genomes]
rs3741627	0.86[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs3759146	0.86[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs3782353	0.86[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs3809147	0.86[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs3825182	0.86[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs3825184	0.86[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs4018510	0.88[ASN][1000 genomes]
rs4237854	0.86[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs4433614	0.86[CHB][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs4526804	0.89[ASN][1000 genomes]
rs4760600	0.86[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs4760661	0.84[ASN][1000 genomes]
rs4760662	0.91[CHB][hapmap];0.91[CHD][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs4760663	0.95[CHB][hapmap];0.95[CHD][hapmap];0.84[JPT][hapmap];0.95[ASN][1000 genomes]
rs4760664	0.89[ASN][1000 genomes]
rs4760665	0.83[ASN][1000 genomes]
rs4760666	0.86[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs4760667	0.81[CHB][hapmap];0.88[ASN][1000 genomes]
rs4760668	0.90[ASN][1000 genomes]
rs58023472	0.84[ASN][1000 genomes]
rs59087236	0.89[ASN][1000 genomes]
rs61941142	0.83[ASN][1000 genomes]
rs61942166	0.88[ASN][1000 genomes]
rs61942167	0.88[ASN][1000 genomes]
rs61942169	0.90[ASN][1000 genomes]
rs61942207	0.89[ASN][1000 genomes]
rs61942209	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6580696	0.86[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs7297958	0.85[CHB][hapmap];0.88[CHD][hapmap];0.84[ASN][1000 genomes]
rs7298330	0.84[ASN][1000 genomes]
rs7304942	0.84[ASN][1000 genomes]
rs7313988	0.89[ASN][1000 genomes]
rs7963018	0.90[ASN][1000 genomes]
rs7963160	0.90[ASN][1000 genomes]
rs7976473	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs833476	0.85[CEU][hapmap]
rs833820	0.96[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs833821	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs833822	0.82[CHB][hapmap];0.86[CHD][hapmap];0.89[ASN][1000 genomes]
rs833827	0.89[ASN][1000 genomes]
rs833828	0.87[ASN][1000 genomes]
rs833839	1.00[ASN][1000 genomes]
rs833841	1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.99[ASN][1000 genomes]
rs833842	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs833843	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]
rs961320	0.83[ASN][1000 genomes]
rs9645813	0.83[ASN][1000 genomes]
rs9783452	0.82[CHB][hapmap];0.86[CHD][hapmap];0.89[ASN][1000 genomes]
rs9783477	0.89[ASN][1000 genomes]
rs9788029	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9795742	0.82[ASN][1000 genomes]
rs9796008	0.84[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs833840	CCDC65	cis	Esophagus Muscularis	GTEx
rs833840	SLC48A1	cis	parietal	SCAN
rs833840	COL2A1	cis	cerebellum	SCAN
rs833840	AQP2	cis	parietal	SCAN
rs833840	PRPH	cis	parietal	SCAN
rs833840	FKBP11	cis	parietal	SCAN
rs833840	ADCY6	cis	parietal	SCAN
rs833840	FKBP11	cis	cerebellum	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49363200-49366200	Bivalent Enhancer	Stomach Mucosa	stomach
2	chr12:49363400-49366200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr12:49363600-49368000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
4	chr12:49363800-49366200	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
5	chr12:49364200-49366600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
6	chr12:49364200-49368000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
7	chr12:49364400-49366400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
8	chr12:49364400-49366400	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
9	chr12:49364800-49366800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr12:49365000-49366400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:49365000-49366400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr12:49365000-49367200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr12:49365200-49366800	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr12:49365400-49367000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
15	chr12:49365400-49367800	Enhancers	HSMMtube	muscle
16	chr12:49365400-49368600	Enhancers	Placenta Amnion	Placenta Amnion
17	chr12:49365600-49366200	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr12:49365600-49366200	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
19	chr12:49365600-49366200	Flanking Active TSS	HSMM	muscle
20	chr12:49365600-49366400	Bivalent Enhancer	Fetal Thymus	thymus
21	chr12:49365600-49366600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
22	chr12:49365600-49367000	Bivalent Enhancer	NHDF-Ad	bronchial
23	chr12:49365600-49367800	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
24	chr12:49365600-49368000	Bivalent Enhancer	Primary hematopoietic stem cells	blood
25	chr12:49365600-49368200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
26	chr12:49365600-49368400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr12:49365600-49368400	Bivalent Enhancer	Placenta	Placenta
28	chr12:49365600-49368600	Bivalent Enhancer	NH-A	brain
29	chr12:49365800-49366200	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr12:49365800-49366200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
31	chr12:49365800-49366200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
32	chr12:49365800-49366200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
33	chr12:49365800-49366200	Bivalent Enhancer	Fetal Stomach	stomach
34	chr12:49365800-49366400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
35	chr12:49365800-49366400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
36	chr12:49365800-49366400	Weak transcription	Right Atrium	heart
37	chr12:49365800-49366600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
38	chr12:49365800-49366600	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
39	chr12:49365800-49366600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
40	chr12:49365800-49366600	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
41	chr12:49365800-49366600	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr12:49365800-49366600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr12:49365800-49366600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr12:49365800-49366800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
45	chr12:49365800-49366800	Bivalent Enhancer	HMEC	breast
46	chr12:49365800-49367000	Bivalent Enhancer	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr12:49365800-49367800	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
48	chr12:49365800-49368000	Bivalent Enhancer	Fetal Muscle Leg	muscle
49	chr12:49365800-49368400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr12:49366000-49366200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell

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