Variant report

Variant	rs10875896
Chromosome Location	chr12:49321935-49321936
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	CEBPB	chr12:49321853-49322000	IMR90	lung:	n/a	n/a
2	GATA2	chr12:49321648-49321976	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:49316917..49319846-chr12:49321799..49325494,4	K562	blood:

Variant related genes	Relation type
ENSG00000201678	TF binding region
FKBP11	TF binding region
ENSG00000134285	Chromatin interaction

Extended variants
information (count: 118 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:115)

rs_ID	r²[population]
rs1051886	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1054376	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10747556	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10747557	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10747558	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10783289	0.89[ASN][1000 genomes]
rs10783290	0.87[ASN][1000 genomes]
rs10783292	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10783293	0.92[ASN][1000 genomes]
rs10783294	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10783295	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10783297	0.88[ASN][1000 genomes]
rs10875886	0.92[ASN][1000 genomes]
rs10875888	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10875892	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10875893	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10875894	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10875895	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10875897	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10875898	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10875900	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10875901	0.87[ASN][1000 genomes]
rs10875902	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1111662	0.89[ASN][1000 genomes]
rs11168779	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11168783	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11168784	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11168785	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11168790	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11168792	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11168794	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11168795	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11168797	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11168798	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11168800	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11168801	0.87[ASN][1000 genomes]
rs11168803	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11168812	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11608916	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11610459	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11610497	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11614474	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12227240	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12228521	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12229275	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12423542	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12579249	0.92[ASN][1000 genomes]
rs1318692	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1690182	0.87[ASN][1000 genomes]
rs1818996	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1830192	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2030900	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2070940	0.87[ASN][1000 genomes]
rs2073480	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2131713	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2272311	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2272312	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2293449	0.92[ASN][1000 genomes]
rs2368701	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2453063	0.88[ASN][1000 genomes]
rs2463175	0.86[ASN][1000 genomes]
rs2641450	0.84[ASN][1000 genomes]
rs2694839	0.87[ASN][1000 genomes]
rs2694840	0.85[ASN][1000 genomes]
rs3741627	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3759146	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3782353	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3809147	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3825182	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3825184	0.91[ASN][1000 genomes]
rs4018510	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4237854	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4433614	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4526804	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4760600	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4760647	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4760661	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4760664	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4760665	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4760666	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4760667	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4760668	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58023472	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59087236	0.87[ASN][1000 genomes]
rs61941142	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61942166	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61942167	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61942169	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61942207	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6580696	0.88[ASN][1000 genomes]
rs7134686	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7297958	0.92[ASN][1000 genomes]
rs7298330	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7304942	0.92[ASN][1000 genomes]
rs7313988	0.87[ASN][1000 genomes]
rs7489036	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7963018	0.88[ASN][1000 genomes]
rs7963160	0.87[ASN][1000 genomes]
rs7976473	0.83[ASN][1000 genomes]
rs833820	0.87[ASN][1000 genomes]
rs833821	0.87[ASN][1000 genomes]
rs833822	0.87[ASN][1000 genomes]
rs833827	0.87[ASN][1000 genomes]
rs833828	0.85[ASN][1000 genomes]
rs833839	0.81[ASN][1000 genomes]
rs833840	0.81[ASN][1000 genomes]
rs833841	0.80[ASN][1000 genomes]
rs833842	0.80[ASN][1000 genomes]
rs961320	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9645813	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9783452	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9783477	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9788029	0.93[ASN][1000 genomes]
rs9795742	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9796008	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10875896	RP11-302B13.1	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49314400-49338000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr12:49314400-49338600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:49319200-49349800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr12:49319400-49325200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr12:49319400-49337800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:49319600-49323200	Weak transcription	Brain Germinal Matrix	brain
7	chr12:49319600-49324400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:49319600-49326600	Weak transcription	Aorta	Aorta
9	chr12:49319600-49331800	Weak transcription	Psoas Muscle	Psoas
10	chr12:49319600-49332800	Weak transcription	Small Intestine	intestine
11	chr12:49319600-49334600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr12:49319800-49322800	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr12:49319800-49322800	Weak transcription	Esophagus	oesophagus
14	chr12:49319800-49322800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr12:49319800-49323000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr12:49319800-49323000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr12:49319800-49323000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr12:49319800-49323000	Weak transcription	Adipose Nuclei	Adipose
19	chr12:49319800-49323000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr12:49319800-49323000	Weak transcription	Colon Smooth Muscle	Colon
21	chr12:49319800-49323000	Weak transcription	Fetal Muscle Leg	muscle
22	chr12:49319800-49323000	Weak transcription	Lung	lung
23	chr12:49319800-49323000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr12:49319800-49323000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr12:49319800-49323000	Weak transcription	HSMM	muscle
26	chr12:49319800-49323200	Weak transcription	Brain Anterior Caudate	brain
27	chr12:49319800-49323200	Weak transcription	Fetal Intestine Large	intestine
28	chr12:49319800-49323200	Weak transcription	Fetal Lung	lung
29	chr12:49319800-49323200	Weak transcription	Left Ventricle	heart
30	chr12:49319800-49323400	Weak transcription	HMEC	breast
31	chr12:49319800-49323400	Weak transcription	NH-A	brain
32	chr12:49319800-49323400	Weak transcription	NHDF-Ad	bronchial
33	chr12:49319800-49324400	Weak transcription	Primary B cells from cord blood	blood
34	chr12:49319800-49324400	Weak transcription	Liver	Liver
35	chr12:49319800-49324400	Weak transcription	Fetal Kidney	kidney
36	chr12:49319800-49324400	Weak transcription	Fetal Muscle Trunk	muscle
37	chr12:49319800-49324400	Weak transcription	Spleen	Spleen
38	chr12:49319800-49325000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr12:49319800-49325000	Weak transcription	Brain Angular Gyrus	brain
40	chr12:49319800-49325000	Weak transcription	Brain Cingulate Gyrus	brain
41	chr12:49319800-49325000	Weak transcription	Brain Hippocampus Middle	brain
42	chr12:49319800-49325000	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr12:49319800-49325000	Weak transcription	Brain Substantia Nigra	brain
44	chr12:49319800-49325000	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr12:49319800-49325000	Weak transcription	Thymus	Thymus
46	chr12:49319800-49326000	Weak transcription	Primary hematopoietic stem cells	blood
47	chr12:49319800-49326200	Weak transcription	Colonic Mucosa	Colon
48	chr12:49319800-49326200	Weak transcription	Duodenum Mucosa	Duodenum
49	chr12:49319800-49326400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr12:49319800-49326400	Weak transcription	Ovary	ovary

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