Variant report

Variant	rs73104143
Chromosome Location	chr12:48087232-48087233
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48082467..48084685-chr12:48086429..48089093,4	K562	blood:
2	chr12:48079504..48082471-chr12:48085134..48087838,3	K562	blood:
3	chr12:48085079..48087645-chr12:48089413..48091227,2	K562	blood:
4	chr12:48085007..48087672-chr12:48089308..48092914,4	K562	blood:
5	chr12:48082733..48084619-chr12:48086537..48089093,2	K562	blood:

Variant related genes	Relation type
ENSG00000005175	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs12422974	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12423045	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12426347	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12426849	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35044089	0.82[EUR][1000 genomes]
rs57848393	0.95[EUR][1000 genomes]
rs67201012	0.95[EUR][1000 genomes]
rs67408202	0.95[EUR][1000 genomes]
rs7303895	0.93[EUR][1000 genomes]
rs7304743	0.93[EUR][1000 genomes]
rs73102120	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73102125	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73102127	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73102140	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73102148	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73102151	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73102166	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73102168	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73102171	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73102188	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73102195	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73102201	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73104103	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73104104	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73104111	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73104115	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73104116	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73104138	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73104144	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73104148	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73104152	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73104155	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73104161	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73104163	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73104177	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs73104184	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs73104188	0.95[EUR][1000 genomes]
rs73104190	1.00[AFR][1000 genomes]
rs73104197	1.00[AFR][1000 genomes]
rs73105818	1.00[AFR][1000 genomes]
rs73105829	1.00[AFR][1000 genomes]
rs73105845	1.00[AFR][1000 genomes]
rs73105847	1.00[AFR][1000 genomes]
rs73111258	0.82[EUR][1000 genomes]
rs73113117	0.82[EUR][1000 genomes]
rs73113139	0.82[EUR][1000 genomes]
rs73113143	0.82[EUR][1000 genomes]
rs73113159	0.89[EUR][1000 genomes]
rs73113161	0.89[EUR][1000 genomes]
rs7954764	0.88[AMR][1000 genomes];0.89[EUR][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	esv2751101	chr12:47940858-48126885	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv695	chr12:48043261-48088221	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs73104143	RP1-197B17.3	cis	Thyroid	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48029800-48098800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:48046600-48087800	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr12:48046600-48090000	Weak transcription	Psoas Muscle	Psoas
4	chr12:48046600-48097000	Weak transcription	Brain Angular Gyrus	brain
5	chr12:48046600-48097600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr12:48046600-48099200	Weak transcription	Gastric	stomach
7	chr12:48046800-48098600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr12:48046800-48099000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr12:48050200-48098600	Weak transcription	Pancreas	Pancrea
10	chr12:48052000-48094400	Weak transcription	Aorta	Aorta
11	chr12:48056000-48099000	Weak transcription	Right Ventricle	heart
12	chr12:48057200-48098800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr12:48058000-48098600	Weak transcription	Colonic Mucosa	Colon
14	chr12:48060400-48088400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr12:48060600-48094200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr12:48060800-48094200	Weak transcription	Brain Cingulate Gyrus	brain
17	chr12:48061600-48088600	Weak transcription	Brain Substantia Nigra	brain
18	chr12:48062600-48094200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr12:48062800-48098600	Weak transcription	Colon Smooth Muscle	Colon
20	chr12:48063000-48099000	Weak transcription	Small Intestine	intestine
21	chr12:48064600-48099200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr12:48064800-48089600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr12:48064800-48090000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr12:48065000-48092800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr12:48068400-48097200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr12:48071800-48091600	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr12:48072800-48090200	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr12:48072800-48091400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr12:48072800-48091600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr12:48073000-48091800	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr12:48073600-48091200	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr12:48074000-48093600	Weak transcription	HMEC	breast
33	chr12:48074000-48095400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr12:48074000-48095800	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr12:48074200-48097000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr12:48074200-48099000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr12:48075600-48087800	Weak transcription	Brain Anterior Caudate	brain
38	chr12:48075600-48088400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr12:48075600-48088600	Weak transcription	Fetal Brain Female	brain
40	chr12:48075600-48089200	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr12:48075600-48090000	Weak transcription	GM12878-XiMat	blood
42	chr12:48075600-48097200	Weak transcription	Left Ventricle	heart
43	chr12:48075600-48098600	Weak transcription	Brain Hippocampus Middle	brain
44	chr12:48076000-48098800	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr12:48077200-48095800	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr12:48077800-48091600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr12:48078200-48090600	Weak transcription	NHDF-Ad	bronchial
48	chr12:48079200-48089000	Strong transcription	Primary B cells from cord blood	blood
49	chr12:48079600-48097600	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr12:48080000-48089800	Weak transcription	Osteobl	bone

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