Variant report

Variant	rs12487977
Chromosome Location	chr3:141642312-141642313
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	POLR2A	chr3:141642158-141642347	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
ATP1B3-AS1	TF binding region

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10755098	0.82[ASN][1000 genomes]
rs10935439	0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs10935440	0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs10935441	0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs10935442	0.82[ASN][1000 genomes]
rs10935443	0.82[ASN][1000 genomes]
rs10935446	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs10935447	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs11569259	0.82[EUR][1000 genomes]
rs11569262	0.82[EUR][1000 genomes]
rs11569278	0.82[EUR][1000 genomes]
rs11569281	0.85[EUR][1000 genomes]
rs11569291	0.85[EUR][1000 genomes]
rs11706195	0.82[ASN][1000 genomes]
rs11707100	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs11707427	0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11710245	0.84[ASN][1000 genomes]
rs11711748	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs11713023	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs11721024	0.82[ASN][1000 genomes]
rs11844	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12486398	0.82[ASN][1000 genomes]
rs12487983	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12490893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12494971	1.00[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12497112	0.90[EUR][1000 genomes]
rs12497443	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16851892	0.82[ASN][1000 genomes]
rs2115935	0.82[ASN][1000 genomes]
rs2288634	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2288635	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2288636	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2861382	0.80[ASN][1000 genomes]
rs34071952	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36038301	0.82[ASN][1000 genomes]
rs3762726	0.90[EUR][1000 genomes]
rs3792410	0.84[ASN][1000 genomes]
rs3792411	0.84[ASN][1000 genomes]
rs3804772	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3804773	0.84[ASN][1000 genomes]
rs3828398	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4683412	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4683413	0.82[EUR][1000 genomes]
rs4683414	0.82[EUR][1000 genomes]
rs4683638	0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs4683639	0.82[ASN][1000 genomes]
rs4683640	0.82[ASN][1000 genomes]
rs4683641	0.82[ASN][1000 genomes]
rs4683642	0.82[ASN][1000 genomes]
rs4683643	0.82[ASN][1000 genomes]
rs4683644	0.82[ASN][1000 genomes]
rs4683646	0.84[ASN][1000 genomes]
rs4683647	0.81[ASN][1000 genomes]
rs4683649	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4683651	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4683652	0.97[EUR][1000 genomes]
rs55945175	0.82[ASN][1000 genomes]
rs59122181	0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs745966	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7616903	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949709	chr3:141295050-142178144	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1013352	chr3:141541105-141870293	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12487977	TFDP2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:141597000-141646400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:141616200-141646600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr3:141616200-141648600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:141619600-141644000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr3:141620800-141646800	Weak transcription	Gastric	stomach
6	chr3:141621000-141646600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr3:141621000-141670800	Weak transcription	Small Intestine	intestine
8	chr3:141622000-141645000	Strong transcription	Dnd41	blood
9	chr3:141622000-141647600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr3:141622400-141647000	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr3:141622600-141644800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:141623600-141652400	Strong transcription	Fetal Thymus	thymus
13	chr3:141624600-141649200	Weak transcription	Brain Substantia Nigra	brain
14	chr3:141625600-141647200	Weak transcription	Liver	Liver
15	chr3:141625600-141668400	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr3:141626600-141659000	Weak transcription	Pancreas	Pancrea
17	chr3:141627400-141646600	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr3:141627600-141646400	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr3:141627600-141649200	Weak transcription	Primary B cells from peripheral blood	blood
20	chr3:141627800-141652600	Weak transcription	Brain Anterior Caudate	brain
21	chr3:141628200-141673600	Weak transcription	Colon Smooth Muscle	Colon
22	chr3:141628600-141646400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr3:141628600-141658800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr3:141628600-141669000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr3:141628800-141646000	Weak transcription	Stomach Smooth Muscle	stomach
26	chr3:141628800-141669800	Weak transcription	Fetal Lung	lung
27	chr3:141628800-141674000	Weak transcription	Brain Hippocampus Middle	brain
28	chr3:141629000-141739200	Weak transcription	Psoas Muscle	Psoas
29	chr3:141630000-141647000	Strong transcription	Primary monocytes fromperipheralblood	blood
30	chr3:141630600-141647400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:141630600-141647400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:141631200-141647600	Strong transcription	Monocytes-CD14+_RO01746	blood
33	chr3:141632000-141644200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr3:141632000-141647400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr3:141632000-141648800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:141632200-141643200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr3:141632200-141643200	Strong transcription	NHEK	skin
38	chr3:141632200-141645000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr3:141632200-141647800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:141632200-141648000	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr3:141632400-141654000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr3:141633000-141659000	Weak transcription	NHLF	lung
43	chr3:141633600-141648000	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr3:141633800-141646000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr3:141634000-141642800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr3:141634000-141643200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr3:141634200-141648600	Weak transcription	Aorta	Aorta
48	chr3:141634200-141682000	Weak transcription	Brain Angular Gyrus	brain
49	chr3:141634400-141648600	Weak transcription	Fetal Kidney	kidney
50	chr3:141634400-141656600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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