Variant report

Variant	rs12464648
Chromosome Location	chr2:113968257-113968258
allele	C/T
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	chr2:113967589-113968540	ECC-1	luminal epithelium:	n/a	n/a
2	POLR2A	chr2:113968208-113968260	HUVEC	blood vessel:	n/a	n/a
3	MAX	chr2:113967936-113970355	A549	lung:	n/a	chr2:113969423-113969433
4	POLR2A	chr2:113966047-113968607	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:113967235..113968789-chr2:113984371..113986823,2	MCF-7	breast:
2	chr2:113031655..113033342-chr2:113967822..113970476,2	K562	blood:
3	chr2:113967701..113970551-chr2:113977130..113979448,2	K562	blood:

Variant related genes	Relation type
PAX8-AS1	TF binding region
ENSG00000188177	Chromatin interaction
ENSG00000125618	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12470761	1.00[ASN][1000 genomes]
rs12994520	1.00[ASN][1000 genomes]
rs17628215	1.00[ASN][1000 genomes]
rs72831831	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997348	chr2:113688093-113986508	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv582711	chr2:113895516-113984503	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv582712	chr2:113932431-113985170	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12464648	LOC654433	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113957200-113969000	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr2:113957200-113969000	Weak transcription	Right Atrium	heart
3	chr2:113957400-113969000	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr2:113957400-113982600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr2:113958000-113975200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:113959200-113968800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr2:113959200-113968800	Weak transcription	K562	blood
8	chr2:113960600-113975200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr2:113960800-113968600	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr2:113960800-113969600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr2:113960800-113974600	Weak transcription	Primary hematopoietic stem cells	blood
12	chr2:113960800-113975000	Weak transcription	Liver	Liver
13	chr2:113961000-113968400	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr2:113962000-113969600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr2:113962200-113968400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr2:113962200-113969000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
17	chr2:113962200-113969400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr2:113962200-113974800	Weak transcription	GM12878-XiMat	blood
19	chr2:113962400-113968800	Weak transcription	Fetal Thymus	thymus
20	chr2:113962600-113974600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr2:113964000-113969000	Weak transcription	Small Intestine	intestine
22	chr2:113964000-113972800	Enhancers	Fetal Kidney	kidney
23	chr2:113964600-113969800	Weak transcription	Pancreas	Pancrea
24	chr2:113964800-113969600	Weak transcription	Fetal Intestine Small	intestine
25	chr2:113965000-113969000	Weak transcription	Fetal Intestine Large	intestine
26	chr2:113966200-113969000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:113966200-113969000	Enhancers	Muscle Satellite Cultured Cells	--
28	chr2:113966200-113969000	Enhancers	HSMM	muscle
29	chr2:113966200-113969200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:113966200-113969800	Enhancers	Esophagus	oesophagus
31	chr2:113966200-113970400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr2:113966200-113972000	Enhancers	Fetal Stomach	stomach
33	chr2:113966400-113968600	Enhancers	HSMMtube	muscle
34	chr2:113966400-113968800	Enhancers	Hela-S3	cervix
35	chr2:113966800-113969400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr2:113967000-113968800	Enhancers	NHEK	skin
37	chr2:113967000-113970000	Enhancers	Colonic Mucosa	Colon
38	chr2:113967000-113970800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr2:113967200-113968400	Weak transcription	NH-A	brain
40	chr2:113967200-113968400	Weak transcription	Osteobl	bone
41	chr2:113967200-113969000	Weak transcription	Rectal Smooth Muscle	rectum
42	chr2:113967200-113971400	Enhancers	Placenta	Placenta
43	chr2:113967400-113968600	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr2:113967400-113968600	Weak transcription	Stomach Mucosa	stomach
45	chr2:113967400-113968600	Enhancers	A549	lung
46	chr2:113967400-113968800	Weak transcription	Fetal Lung	lung
47	chr2:113967400-113969000	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr2:113967400-113969000	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr2:113967400-113969200	Enhancers	Stomach Smooth Muscle	stomach
50	chr2:113967400-113971200	Weak transcription	Thymus	Thymus

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