Variant report

Variant	rs833839
Chromosome Location	chr12:49366890-49366891
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr12:49366440-49366896	MCF-7	breast:	n/a	n/a
2	CTCF	chr12:49366536-49366907	MCF-7	breast:	n/a	n/a
3	MAX	chr12:49364845-49367135	NB4	blood:	n/a	chr12:49364858-49364868 chr12:49365173-49365183 chr12:49366530-49366539
4	CTCF	chr12:49366740-49366890	GM12872	blood:	n/a	n/a
5	RAD21	chr12:49366555-49366951	MCF-7	breast:	n/a	n/a
6	RAD21	chr12:49366544-49366925	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49366194..49369077-chr12:49377220..49379959,3	K562	blood:
2	chr12:49365653..49367190-chr12:49391063..49393227,2	K562	blood:
3	chr12:49348867..49353149-chr12:49362475..49369316,15	MCF-7	breast:
4	chr12:49365267..49367565-chr12:49453514..49456197,2	K562	blood:
5	chr12:49366322..49367318-chr12:49381527..49382472,4	MCF-7	breast:
6	chr12:49366496..49367129-chr12:49388953..49389723,2	MCF-7	breast:
7	chr12:49365293..49369225-chr12:49386844..49389863,3	MCF-7	breast:
8	chr12:49365791..49367365-chr12:49376844..49379494,2	MCF-7	breast:

No data

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

Extended variants
information (count: 124 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs1051886	0.90[ASN][1000 genomes]
rs1054376	0.88[ASN][1000 genomes]
rs10747556	0.83[ASN][1000 genomes]
rs10747557	0.88[ASN][1000 genomes]
rs10747558	0.89[ASN][1000 genomes]
rs10783287	0.93[CEU][hapmap]
rs10783289	0.83[ASN][1000 genomes]
rs10783293	0.84[ASN][1000 genomes]
rs10783294	0.84[ASN][1000 genomes]
rs10783295	0.84[ASN][1000 genomes]
rs10783297	0.88[ASN][1000 genomes]
rs10875886	0.83[ASN][1000 genomes]
rs10875893	0.82[ASN][1000 genomes]
rs10875894	0.84[ASN][1000 genomes]
rs10875895	0.84[ASN][1000 genomes]
rs10875896	0.81[ASN][1000 genomes]
rs10875897	0.88[ASN][1000 genomes]
rs10875898	0.88[ASN][1000 genomes]
rs10875899	0.82[ASN][1000 genomes]
rs10875900	0.90[ASN][1000 genomes]
rs10875901	0.89[ASN][1000 genomes]
rs10875902	0.88[ASN][1000 genomes]
rs1111662	0.88[ASN][1000 genomes]
rs11168779	0.83[ASN][1000 genomes]
rs11168783	0.83[ASN][1000 genomes]
rs11168784	0.83[ASN][1000 genomes]
rs11168785	0.84[ASN][1000 genomes]
rs11168790	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	0.83[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[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	0.88[ASN][1000 genomes]
rs2030900	0.88[ASN][1000 genomes]
rs2070940	0.88[ASN][1000 genomes]
rs2073480	0.88[ASN][1000 genomes]
rs2131713	0.88[ASN][1000 genomes]
rs2272311	0.87[ASN][1000 genomes]
rs2272312	0.85[ASN][1000 genomes]
rs2293449	0.82[CEU][hapmap];0.86[ASN][1000 genomes]
rs2368701	0.83[ASN][1000 genomes]
rs2446999	0.92[CEU][hapmap]
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]
rs2926806	0.92[CEU][hapmap]
rs2934998	0.92[CEU][hapmap]
rs3741627	0.90[ASN][1000 genomes]
rs3759146	0.85[ASN][1000 genomes]
rs3782353	0.90[ASN][1000 genomes]
rs3809147	0.83[ASN][1000 genomes]
rs3825182	0.85[ASN][1000 genomes]
rs3825184	0.83[ASN][1000 genomes]
rs4018510	0.88[ASN][1000 genomes]
rs4237854	0.86[ASN][1000 genomes]
rs4433614	0.83[ASN][1000 genomes]
rs4526804	0.89[ASN][1000 genomes]
rs4760600	0.83[ASN][1000 genomes]
rs4760661	0.84[ASN][1000 genomes]
rs4760662	0.92[ASN][1000 genomes]
rs4760663	0.95[ASN][1000 genomes]
rs4760664	0.89[ASN][1000 genomes]
rs4760665	0.83[ASN][1000 genomes]
rs4760666	0.87[ASN][1000 genomes]
rs4760667	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	0.83[ASN][1000 genomes]
rs6580696	0.90[ASN][1000 genomes]
rs7297958	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	0.90[ASN][1000 genomes]
rs833483	0.92[CEU][hapmap]
rs833484	0.93[CEU][hapmap]
rs833820	0.91[ASN][1000 genomes]
rs833821	0.91[ASN][1000 genomes]
rs833822	0.89[ASN][1000 genomes]
rs833827	0.89[ASN][1000 genomes]
rs833828	0.87[ASN][1000 genomes]
rs833840	1.00[ASN][1000 genomes]
rs833841	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs833842	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs833843	0.94[ASN][1000 genomes]
rs961320	0.83[ASN][1000 genomes]
rs9645813	0.83[ASN][1000 genomes]
rs9783452	0.89[ASN][1000 genomes]
rs9783477	0.89[ASN][1000 genomes]
rs9788029	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs833839	FKBP11	cis	Frontal Cortex	GTEx
rs833839	CCDC65	cis	Thyroid	GTEx
rs833839	CCDC65	cis	Esophagus Muscularis	GTEx

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49363600-49368000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
2	chr12:49364200-49368000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
3	chr12:49365000-49367200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr12:49365400-49367000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
5	chr12:49365400-49367800	Enhancers	HSMMtube	muscle
6	chr12:49365400-49368600	Enhancers	Placenta Amnion	Placenta Amnion
7	chr12:49365600-49367000	Bivalent Enhancer	NHDF-Ad	bronchial
8	chr12:49365600-49367800	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
9	chr12:49365600-49368000	Bivalent Enhancer	Primary hematopoietic stem cells	blood
10	chr12:49365600-49368200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
11	chr12:49365600-49368400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr12:49365600-49368400	Bivalent Enhancer	Placenta	Placenta
13	chr12:49365600-49368600	Bivalent Enhancer	NH-A	brain
14	chr12:49365800-49367000	Bivalent Enhancer	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr12:49365800-49367800	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
16	chr12:49365800-49368000	Bivalent Enhancer	Fetal Muscle Leg	muscle
17	chr12:49365800-49368400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr12:49366000-49367600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
19	chr12:49366000-49367600	Weak transcription	A549	lung
20	chr12:49366000-49368000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr12:49366000-49368400	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
22	chr12:49366000-49371000	Weak transcription	Pancreas	Pancrea
23	chr12:49366200-49368000	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr12:49366200-49368000	Enhancers	HSMM	muscle
25	chr12:49366400-49367200	Weak transcription	Spleen	Spleen
26	chr12:49366400-49367600	Enhancers	Osteobl	bone
27	chr12:49366400-49367800	Enhancers	Right Atrium	heart
28	chr12:49366400-49368200	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
29	chr12:49366600-49367200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr12:49366800-49367000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
31	chr12:49366800-49367000	Enhancers	K562	blood
32	chr12:49366800-49367200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr12:49366800-49367800	Bivalent Enhancer	Adipose Nuclei	Adipose
34	chr12:49366800-49368400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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