Variant report

Variant	rs10877864
Chromosome Location	chr12:62893199-62893200
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:62892704..62894662-chr12:62995139..62997140,2	K562	blood:

Variant related genes	Relation type
ENSG00000257354	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10444576	1.00[JPT][hapmap]
rs10877855	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877857	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877859	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877862	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10877870	0.93[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174487	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11174494	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174495	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174496	0.91[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174498	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174517	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174527	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174537	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11174557	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11174562	0.82[AFR][1000 genomes]
rs11174568	0.91[AFR][1000 genomes]
rs11174571	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes]
rs11174575	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes]
rs11520127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11613132	0.93[CEU][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11614022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11614822	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12367878	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes]
rs12369751	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes]
rs12369961	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12369985	1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12370404	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17716977	1.00[CHB][hapmap]
rs17731893	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes]
rs17732089	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.82[AFR][1000 genomes]
rs17732182	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes]
rs2270732	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs55833440	0.82[AFR][1000 genomes]
rs7296573	1.00[ASW][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.91[AFR][1000 genomes]
rs7297093	1.00[JPT][hapmap];0.91[AFR][1000 genomes]
rs7301016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7302094	1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7302456	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7303825	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311952	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs73124315	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73126004	0.82[AFR][1000 genomes]
rs73126024	0.91[AFR][1000 genomes]
rs73141014	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73141045	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7962519	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975109	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[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	nsv530690	chr12:62678463-62999462	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
2	nsv899158	chr12:62783967-62937259	Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv899159	chr12:62783967-62945245	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv821671	chr12:62794304-63007964	Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv469418	chr12:62893199-62959137	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
6	nsv559156	chr12:62893199-62959137	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10877864	TBK1	cis	parietal	SCAN
rs10877864	MON2	cis	parietal	SCAN
rs10877864	MON2	cis	cerebellum	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:62861800-62902200	Weak transcription	Fetal Kidney	kidney
2	chr12:62862800-62895400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr12:62863200-62895200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr12:62863200-62896800	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr12:62863200-62901800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr12:62863200-62937400	Weak transcription	Pancreas	Pancrea
7	chr12:62863400-62895400	Weak transcription	Stomach Smooth Muscle	stomach
8	chr12:62863400-62902000	Weak transcription	HUVEC	blood vessel
9	chr12:62863400-62911000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr12:62863600-62926400	Weak transcription	Colon Smooth Muscle	Colon
11	chr12:62864000-62894400	Weak transcription	Spleen	Spleen
12	chr12:62864000-62899200	Weak transcription	Brain Germinal Matrix	brain
13	chr12:62864000-62901600	Weak transcription	Lung	lung
14	chr12:62864000-62901600	Weak transcription	Rectal Smooth Muscle	rectum
15	chr12:62864000-62906200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr12:62866000-62895400	Weak transcription	Left Ventricle	heart
17	chr12:62866200-62897000	Weak transcription	K562	blood
18	chr12:62866200-62899200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr12:62866200-62906200	Weak transcription	Aorta	Aorta
20	chr12:62866600-62896000	Weak transcription	Fetal Brain Female	brain
21	chr12:62866600-62906200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr12:62866600-62912400	Weak transcription	NHLF	lung
23	chr12:62866600-62953200	Weak transcription	Psoas Muscle	Psoas
24	chr12:62867200-62898600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr12:62869000-62904400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr12:62871000-62910800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr12:62871200-62895200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr12:62871800-62895200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr12:62871800-62895400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr12:62871800-62897200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr12:62871800-62926200	Weak transcription	Fetal Brain Male	brain
32	chr12:62872000-62894200	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr12:62872200-62895400	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr12:62872600-62901600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr12:62873400-62895400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr12:62874000-62895800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr12:62874600-62898800	Weak transcription	Fetal Muscle Trunk	muscle
38	chr12:62874600-62917400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr12:62874800-62895200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr12:62874800-62896000	Weak transcription	HMEC	breast
41	chr12:62875600-62901200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr12:62876000-62902000	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr12:62876000-62905800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr12:62876000-62937400	Weak transcription	Gastric	stomach
45	chr12:62876200-62895600	Weak transcription	HSMM	muscle
46	chr12:62876200-62913000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr12:62876400-62902000	Weak transcription	Brain Anterior Caudate	brain
48	chr12:62876800-62897000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr12:62877400-62899200	Weak transcription	Ovary	ovary
50	chr12:62877800-62896800	Weak transcription	Brain Hippocampus Middle	brain

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