Variant report

Variant	rs16917969
Chromosome Location	chr12:9222063-9222064
allele	A/C
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	chr12:9216895-9230988	HepG2	liver:	n/a	n/a
2	GATA3	chr12:9221931-9222119	SH-SY5Y	brain:	n/a	n/a
3	POLR2A	chr12:9221907-9222942	HepG2	liver:	n/a	n/a
4	POLR2A	chr12:9221119-9222115	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
LINC00612	TF binding region
A2M	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10492113	1.00[MEX][hapmap]
rs12304948	1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs16918015	1.00[EUR][1000 genomes]
rs16918023	1.00[EUR][1000 genomes]
rs16918152	1.00[MEX][hapmap]
rs226409	1.00[EUR][1000 genomes]
rs226412	1.00[EUR][1000 genomes]
rs226413	1.00[EUR][1000 genomes]
rs3026250	1.00[ASW][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.91[YRI][hapmap]
rs41393747	1.00[MEX][hapmap]
rs56016864	1.00[EUR][1000 genomes]
rs7298071	1.00[EUR][1000 genomes]
rs7303415	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74060475	1.00[EUR][1000 genomes]
rs74060548	1.00[EUR][1000 genomes]
rs74060552	1.00[EUR][1000 genomes]
rs74061408	1.00[EUR][1000 genomes]
rs74061424	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7957038	1.00[GIH][hapmap];1.00[MEX][hapmap]
rs7980288	1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832327	chr12:9081779-9246220	Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	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
3	nsv898738	chr12:9205030-9274394	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16917969	CLEC4D	cis	lymphoblastoid	seeQTL

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9217400-9223400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr12:9217600-9223200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr12:9217800-9225000	Weak transcription	Small Intestine	intestine
4	chr12:9217800-9234200	Weak transcription	Primary T cells from cord blood	blood
5	chr12:9218000-9226800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr12:9218000-9234000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr12:9218200-9223000	Weak transcription	Aorta	Aorta
8	chr12:9218200-9223200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr12:9218200-9224200	Weak transcription	Ovary	ovary
10	chr12:9218200-9232200	Weak transcription	Fetal Muscle Leg	muscle
11	chr12:9218200-9236200	Weak transcription	Psoas Muscle	Psoas
12	chr12:9218200-9266200	Weak transcription	Fetal Kidney	kidney
13	chr12:9218400-9223800	Weak transcription	Duodenum Mucosa	Duodenum
14	chr12:9218400-9224200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr12:9218400-9224200	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr12:9218400-9224600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr12:9218400-9228600	Weak transcription	Brain Anterior Caudate	brain
18	chr12:9218400-9230800	Weak transcription	Brain Hippocampus Middle	brain
19	chr12:9218400-9231000	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr12:9218400-9234400	Weak transcription	Right Atrium	heart
21	chr12:9218400-9236600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr12:9218400-9236600	Weak transcription	Brain Substantia Nigra	brain
23	chr12:9218400-9237200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr12:9218600-9225000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr12:9218600-9229400	Weak transcription	Colonic Mucosa	Colon
26	chr12:9218600-9235600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr12:9218600-9235800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:9218600-9236400	Weak transcription	Brain Angular Gyrus	brain
29	chr12:9218800-9225000	Weak transcription	Rectal Smooth Muscle	rectum
30	chr12:9218800-9230400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr12:9218800-9236200	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr12:9218800-9236200	Weak transcription	Fetal Heart	heart
33	chr12:9219000-9223000	Weak transcription	Spleen	Spleen
34	chr12:9219000-9224000	Weak transcription	Colon Smooth Muscle	Colon
35	chr12:9219000-9233200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr12:9219200-9223600	Weak transcription	Fetal Stomach	stomach
37	chr12:9219200-9224200	Weak transcription	Right Ventricle	heart
38	chr12:9219200-9225000	Weak transcription	Lung	lung
39	chr12:9219200-9226400	Weak transcription	Pancreas	Pancrea
40	chr12:9219200-9229200	Weak transcription	Gastric	stomach
41	chr12:9219200-9234600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr12:9219200-9266000	Weak transcription	Esophagus	oesophagus
43	chr12:9219400-9233200	Strong transcription	Stomach Smooth Muscle	stomach
44	chr12:9219600-9224600	Weak transcription	Fetal Intestine Large	intestine
45	chr12:9219800-9222200	Strong transcription	Liver	Liver
46	chr12:9219800-9225200	Strong transcription	Adipose Nuclei	Adipose
47	chr12:9219800-9233200	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr12:9219800-9235800	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr12:9220000-9224800	Weak transcription	Fetal Intestine Small	intestine
50	chr12:9220200-9225000	Strong transcription	HepG2	liver

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