Variant report

Variant	rs10875976
Chromosome Location	chr12:50226467-50226468
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr12:50226090-50227106	K562	blood:	n/a	n/a
2	POLR2A	chr12:50226439-50227013	U87	brain:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:50134678..50136845-chr12:50226135..50228888,2	K562	blood:
2	chr12:50225491..50228236-chr12:50228329..50230390,4	MCF-7	breast:
3	chr12:50220112..50224669-chr12:50225407..50232096,10	K562	blood:
4	chr12:50193481..50196503-chr12:50223666..50226555,3	MCF-7	breast:
5	chr12:50224798..50226828-chr12:50232751..50234634,3	K562	blood:
6	chr12:50168654..50171437-chr12:50224494..50226796,2	MCF-7	breast:
7	chr12:50190258..50192512-chr12:50224620..50227026,2	K562	blood:

No data

Variant related genes	Relation type
NCKAP5L	TF binding region
ENSG00000167566	Chromatin interaction
ENSG00000258057	Chromatin interaction
ENSG00000139644	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1031477	0.89[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap];0.93[ASN][1000 genomes]
rs11169166	0.92[ASN][1000 genomes]
rs11169170	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4898534	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4898535	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55677077	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66908137	0.88[EUR][1000 genomes]
rs7953539	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973894	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[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	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
3	nsv522972	chr12:50196394-50410831	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Obesity	23563607	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10875976	RPAP3	cis	parietal	SCAN
rs10875976	LALBA	cis	cerebellum	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50222800-50235400	Weak transcription	Ovary	ovary
2	chr12:50222800-50236200	Weak transcription	Aorta	Aorta
3	chr12:50223000-50231800	Weak transcription	Pancreas	Pancrea
4	chr12:50223000-50232000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr12:50223000-50234600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr12:50223000-50234600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr12:50223000-50235000	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr12:50223000-50235400	Weak transcription	Brain Anterior Caudate	brain
9	chr12:50223000-50235400	Weak transcription	Left Ventricle	heart
10	chr12:50223000-50235600	Weak transcription	Brain Substantia Nigra	brain
11	chr12:50223000-50236000	Weak transcription	Lung	lung
12	chr12:50223200-50226600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr12:50223200-50226800	Weak transcription	NH-A	brain
14	chr12:50223200-50231800	Weak transcription	Brain Hippocampus Middle	brain
15	chr12:50223200-50232000	Weak transcription	NHLF	lung
16	chr12:50223200-50235200	Weak transcription	Primary hematopoietic stem cells	blood
17	chr12:50223200-50235200	Weak transcription	Liver	Liver
18	chr12:50223200-50235200	Weak transcription	HSMM	muscle
19	chr12:50223200-50235400	Weak transcription	Primary neutrophils fromperipheralblood	blood
20	chr12:50223200-50235400	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr12:50223200-50235400	Weak transcription	Adipose Nuclei	Adipose
22	chr12:50223200-50235400	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr12:50223200-50235400	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr12:50223200-50235400	Weak transcription	Thymus	Thymus
25	chr12:50223200-50235400	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr12:50223200-50235400	Weak transcription	NHDF-Ad	bronchial
27	chr12:50223200-50235600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr12:50223400-50231800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr12:50223400-50231800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr12:50223400-50231800	Weak transcription	Stomach Smooth Muscle	stomach
31	chr12:50223400-50232000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr12:50223400-50232000	Weak transcription	Fetal Muscle Leg	muscle
33	chr12:50223400-50232200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:50223400-50232600	Weak transcription	Fetal Thymus	thymus
35	chr12:50223400-50233200	Weak transcription	A549	lung
36	chr12:50223400-50234600	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr12:50223400-50235000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr12:50223400-50235000	Weak transcription	Primary T cells from cord blood	blood
39	chr12:50223400-50235000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr12:50223400-50235000	Weak transcription	Hela-S3	cervix
41	chr12:50223400-50235200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr12:50223400-50235200	Weak transcription	Primary B cells from peripheral blood	blood
43	chr12:50223400-50235200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr12:50223400-50235200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr12:50223400-50235200	Weak transcription	Colon Smooth Muscle	Colon
46	chr12:50223400-50235200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr12:50223400-50235200	Weak transcription	Fetal Intestine Large	intestine
48	chr12:50223400-50235200	Weak transcription	Fetal Intestine Small	intestine
49	chr12:50223400-50235200	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr12:50223400-50235400	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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