Variant report

Variant	rs9971685
Chromosome Location	chr12:9459854-9459855
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs10743654	0.89[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10843383	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045317	chr12:9113216-9544655	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
2	nsv1048491	chr12:9208806-9544655	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats 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	35 gene(s)	inside rSNPs	diseases
3	nsv523958	chr12:9303440-9549072	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
4	nsv557355	chr12:9309995-9529015	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1035953	chr12:9314481-9544655	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
6	nsv427903	chr12:9371593-9830668	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
7	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
8	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
9	nsv916832	chr12:9397450-9693952	ZNF genes & repeats Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv976736	chr12:9431362-9524845	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv898740	chr12:9436446-9546962	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv1050161	chr12:9436635-9685768	Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
13	nsv975441	chr12:9439756-9469779	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv898741	chr12:9458525-9546962	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9971685	RP11-22B23.1	cis	Muscle Skeletal	GTEx
rs9971685	DDX12P	cis	Muscle Skeletal	GTEx
rs9971685	RP11-22B23.1	cis	Whole Blood	GTEx
rs9971685	RP11-22B23.1	cis	Artery Tibial	GTEx
rs9971685	RP11-22B23.1	cis	lung	GTEx

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9435400-9464000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr12:9436200-9460000	Weak transcription	Fetal Lung	lung
3	chr12:9436400-9464000	Weak transcription	Thymus	Thymus
4	chr12:9437200-9460600	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr12:9437200-9461200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr12:9437200-9462800	Weak transcription	Esophagus	oesophagus
7	chr12:9437200-9465600	Weak transcription	Ovary	ovary
8	chr12:9437200-9467600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr12:9437200-9472400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr12:9437200-9485200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:9437400-9467800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr12:9437400-9468000	Weak transcription	Pancreas	Pancrea
13	chr12:9437400-9470800	Weak transcription	Brain Germinal Matrix	brain
14	chr12:9437800-9462600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr12:9437800-9463800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr12:9437800-9464000	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr12:9443200-9467800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr12:9445800-9464000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr12:9446200-9466000	Weak transcription	Fetal Brain Female	brain
20	chr12:9449000-9460000	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr12:9449000-9460200	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr12:9449000-9466000	Weak transcription	Gastric	stomach
23	chr12:9449400-9468000	Weak transcription	Stomach Smooth Muscle	stomach
24	chr12:9450200-9462000	Weak transcription	Left Ventricle	heart
25	chr12:9450200-9471400	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr12:9452200-9462800	Weak transcription	Lung	lung
27	chr12:9452400-9466600	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr12:9453200-9464000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr12:9453600-9465200	Weak transcription	Colonic Mucosa	Colon
30	chr12:9455200-9466000	Weak transcription	Fetal Intestine Large	intestine
31	chr12:9455200-9466000	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr12:9455600-9460200	Weak transcription	Brain Hippocampus Middle	brain
33	chr12:9455600-9462600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr12:9455600-9463400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr12:9455800-9461200	Strong transcription	Fetal Stomach	stomach
36	chr12:9455800-9466000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr12:9456200-9461000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr12:9456200-9472200	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr12:9456400-9462000	Weak transcription	Primary B cells from cord blood	blood
40	chr12:9456400-9462800	Weak transcription	Rectal Smooth Muscle	rectum
41	chr12:9456400-9465200	Weak transcription	HepG2	liver
42	chr12:9456400-9471800	Weak transcription	GM12878-XiMat	blood
43	chr12:9456600-9460600	Strong transcription	Dnd41	blood
44	chr12:9456800-9460600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr12:9456800-9466400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr12:9457000-9460200	Strong transcription	Fetal Intestine Small	intestine
47	chr12:9457000-9460800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr12:9457200-9464000	Weak transcription	Fetal Muscle Trunk	muscle
49	chr12:9457400-9463800	Weak transcription	Spleen	Spleen
50	chr12:9457400-9485800	Weak transcription	Primary hematopoietic stem cells	blood

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