Variant report

Variant	rs73104115
Chromosome Location	chr12:48078626-48078627
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	chr12:48076547..48079289-chr12:48099321..48101078,2	K562	blood:

Variant related genes	Relation type
ENSG00000005175	Chromatin interaction
ENSG00000257433	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12422974	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12423045	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12425816	0.81[AFR][1000 genomes]
rs12426347	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12426849	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35044089	0.82[EUR][1000 genomes]
rs35784744	0.81[AFR][1000 genomes]
rs57848393	0.87[EUR][1000 genomes]
rs67201012	0.87[EUR][1000 genomes]
rs67408202	0.87[EUR][1000 genomes]
rs7303895	1.00[EUR][1000 genomes]
rs7304743	1.00[EUR][1000 genomes]
rs73102120	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73102125	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73102127	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73102140	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73102148	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73102151	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73102166	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73102168	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73102171	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73102188	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73102195	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73102201	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73104103	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73104104	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73104111	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73104116	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73104138	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73104143	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73104144	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73104148	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73104152	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73104155	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73104161	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73104163	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73104177	0.87[EUR][1000 genomes]
rs73104184	0.87[EUR][1000 genomes]
rs73104188	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs73105803	0.81[AFR][1000 genomes]
rs73105812	0.81[AFR][1000 genomes]
rs73105814	0.81[AFR][1000 genomes]
rs73105819	0.81[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];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv430507	chr12:47883933-48079507	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	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
3	nsv1050043	chr12:47949004-48087218	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv899058	chr12:48012390-48082482	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	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
rs73104115	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	chr12:48031000-48083200	Weak transcription	Esophagus	oesophagus
3	chr12:48040600-48086000	Weak transcription	Fetal Brain Male	brain
4	chr12:48043400-48080000	Weak transcription	NHEK	skin
5	chr12:48045200-48079200	Weak transcription	NHLF	lung
6	chr12:48046600-48083000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr12:48046600-48087800	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr12:48046600-48090000	Weak transcription	Psoas Muscle	Psoas
9	chr12:48046600-48097000	Weak transcription	Brain Angular Gyrus	brain
10	chr12:48046600-48097600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr12:48046600-48099200	Weak transcription	Gastric	stomach
12	chr12:48046800-48079200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr12:48046800-48083200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr12:48046800-48098600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr12:48046800-48099000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr12:48050200-48098600	Weak transcription	Pancreas	Pancrea
17	chr12:48052000-48094400	Weak transcription	Aorta	Aorta
18	chr12:48055200-48083200	Weak transcription	Brain Germinal Matrix	brain
19	chr12:48056000-48099000	Weak transcription	Right Ventricle	heart
20	chr12:48057200-48098800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr12:48058000-48098600	Weak transcription	Colonic Mucosa	Colon
22	chr12:48058200-48086000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr12:48058600-48082600	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr12:48058800-48086000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:48059800-48083000	Weak transcription	Fetal Intestine Small	intestine
26	chr12:48059800-48083200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr12:48060400-48083000	Weak transcription	Spleen	Spleen
28	chr12:48060400-48088400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr12:48060600-48083000	Weak transcription	Fetal Stomach	stomach
30	chr12:48060600-48084200	Weak transcription	Thymus	Thymus
31	chr12:48060600-48086000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr12:48060600-48094200	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr12:48060800-48094200	Weak transcription	Brain Cingulate Gyrus	brain
34	chr12:48061600-48088600	Weak transcription	Brain Substantia Nigra	brain
35	chr12:48062000-48083200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr12:48062600-48094200	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr12:48062800-48098600	Weak transcription	Colon Smooth Muscle	Colon
38	chr12:48063000-48086400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr12:48063000-48099000	Weak transcription	Small Intestine	intestine
40	chr12:48064600-48086000	Weak transcription	Lung	lung
41	chr12:48064600-48086000	Weak transcription	HSMMtube	muscle
42	chr12:48064600-48099200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr12:48064800-48089600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr12:48064800-48090000	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr12:48065000-48092800	Weak transcription	Stomach Smooth Muscle	stomach
46	chr12:48065200-48079200	Weak transcription	Placenta	Placenta
47	chr12:48066400-48086000	Weak transcription	Fetal Heart	heart
48	chr12:48068400-48083200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr12:48068400-48097200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
50	chr12:48071200-48080200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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