Variant report

Variant	rs12905422
Chromosome Location	chr15:59280279-59280280
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1693534	0.89[CEU][hapmap];0.89[GIH][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs2899637	0.83[CEU][hapmap];0.81[TSI][hapmap]
rs7171316	0.83[CEU][hapmap]
rs8024549	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34110	chr15:58949991-59381634	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
3	esv1850946	chr15:59174539-59429160	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
4	nsv904271	chr15:59249584-59393011	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv520679	chr15:59268410-59376531	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv520872	chr15:59268410-59395184	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12905422	FAM63B	cis	parietal	SCAN
rs12905422	GCNT3	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59278800-59281400	Active TSS	Psoas Muscle	Psoas
2	chr15:59279000-59280400	Active TSS	Skeletal Muscle Female	skeletal muscle
3	chr15:59279000-59281200	Active TSS	Rectal Mucosa Donor 31	rectum
4	chr15:59279000-59281400	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr15:59279000-59281400	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr15:59279000-59281400	Active TSS	Stomach Smooth Muscle	stomach
7	chr15:59279000-59281800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr15:59279000-59281800	Active TSS	K562	blood
9	chr15:59279200-59280400	Active TSS	Colonic Mucosa	Colon
10	chr15:59279200-59280800	Active TSS	iPS-18 Cell Line	embryonic stem cell
11	chr15:59279200-59280800	Active TSS	Esophagus	oesophagus
12	chr15:59279200-59281000	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr15:59279200-59281000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr15:59279200-59281000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
15	chr15:59279200-59281000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr15:59279200-59281000	Active TSS	Brain Angular Gyrus	brain
17	chr15:59279200-59281000	Active TSS	Brain Cingulate Gyrus	brain
18	chr15:59279200-59281000	Active TSS	Sigmoid Colon	Sigmoid Colon
19	chr15:59279200-59281200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr15:59279200-59281200	Active TSS	H9 Cell Line	embryonic stem cell
21	chr15:59279200-59281200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr15:59279200-59281200	Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr15:59279200-59281200	Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr15:59279200-59281200	Active TSS	Primary T cells fromperipheralblood	blood
25	chr15:59279200-59281200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr15:59279200-59281200	Active TSS	Brain Anterior Caudate	brain
27	chr15:59279200-59281200	Active TSS	Brain Hippocampus Middle	brain
28	chr15:59279200-59281200	Active TSS	Brain Inferior Temporal Lobe	brain
29	chr15:59279200-59281200	Active TSS	Colon Smooth Muscle	Colon
30	chr15:59279200-59281200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
31	chr15:59279200-59281200	Active TSS	Fetal Intestine Small	intestine
32	chr15:59279200-59281200	Active TSS	Fetal Muscle Trunk	muscle
33	chr15:59279200-59281400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr15:59279200-59281400	Active TSS	Brain Substantia Nigra	brain
35	chr15:59279200-59281400	Active TSS	Ovary	ovary
36	chr15:59279200-59281400	Active TSS	Right Ventricle	heart
37	chr15:59279200-59281400	Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr15:59279200-59281600	Active TSS	HUES6 Cell Line	embryonic stem cell
39	chr15:59279200-59281600	Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr15:59279200-59281600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr15:59279200-59281600	Active TSS	NHDF-Ad	bronchial
42	chr15:59279200-59281800	Active TSS	ES-I3 Cell Line	embryonic stem cell
43	chr15:59279200-59281800	Active TSS	H1 Cell Line	embryonic stem cell
44	chr15:59279200-59281800	Active TSS	Muscle Satellite Cultured Cells	--
45	chr15:59279200-59281800	Active TSS	Aorta	Aorta
46	chr15:59279200-59281800	Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr15:59279200-59281800	Active TSS	Fetal Stomach	stomach
48	chr15:59279200-59282000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr15:59279200-59282000	Active TSS	Fetal Intestine Large	intestine
50	chr15:59279200-59282000	Active TSS	Fetal Kidney	kidney

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