Variant report

Variant	rs12300053
Chromosome Location	chr12:49735659-49735660
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	CTBP2	chr12:49735158-49737394	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr12:49735652-49736961	SK-N-SH	brain:	n/a	chr12:49736209-49736222 chr12:49736484-49736497 chr12:49736140-49736153 chr12:49736379-49736388 chr12:49736742-49736755 chr12:49736885-49736898 chr12:49736374-49736390 chr12:49736368-49736389 chr12:49736373-49736391 chr12:49736375-49736388 chr12:49736376-49736386 chr12:49736375-49736388 chr12:49736484-49736497
3	HMGN3	chr12:49735645-49736496	K562	blood:	n/a	n/a
4	SIN3A	chr12:49735631-49737614	H1-hESC	embryonic stem cell:	n/a	chr12:49737000-49737013 chr12:49737455-49737463 chr12:49735808-49735821

No.	Distal block	Cell Line	Cell type
1	chr12:49734512..49737434-chr12:49761201..49764804,3	K562	blood:
2	chr12:49656587..49660636-chr12:49733539..49743833,13	K562	blood:
3	chr12:49680691..49694205-chr12:49725987..49738512,25	K562	blood:
4	chr12:49691342..49692923-chr12:49735601..49736627,8	MCF-7	breast:
5	chr12:49720134..49722975-chr12:49734541..49736256,2	MCF-7	breast:
6	chr12:49667825..49672911-chr12:49731373..49736764,7	K562	blood:
7	chr12:49655321..49661148-chr12:49729487..49743115,26	K562	blood:
8	chr12:49685452..49688091-chr12:49734714..49737225,2	MCF-7	breast:
9	chr12:49662709..49665978-chr12:49735321..49738677,4	K562	blood:
10	chr12:49735114..49738057-chr12:49759505..49762701,3	K562	blood:
11	chr12:49666079..49671115-chr12:49733959..49736436,6	K562	blood:
12	chr12:49665205..49667144-chr12:49734147..49736854,2	MCF-7	breast:
13	chr12:49661766..49665978-chr12:49735321..49738677,5	K562	blood:

Variant related genes	Relation type
C1QL4	TF binding region
ENSG00000258101	Chromatin interaction
ENSG00000123352	Chromatin interaction
ENSG00000135406	Chromatin interaction
ENSG00000135451	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000258232	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10467104	1.00[AFR][1000 genomes]
rs11168994	1.00[AFR][1000 genomes]
rs11169030	1.00[AFR][1000 genomes]
rs11169036	1.00[AFR][1000 genomes]
rs11169072	1.00[AFR][1000 genomes]
rs11169077	1.00[AFR][1000 genomes]
rs12297088	1.00[AFR][1000 genomes]
rs12305870	1.00[AFR][1000 genomes]
rs12309765	1.00[AFR][1000 genomes]
rs12322175	1.00[AFR][1000 genomes]
rs12322207	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv428801	chr12:49536659-49744884	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
5	nsv1042122	chr12:49678529-49823168	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
6	nsv1039176	chr12:49678529-49832618	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
7	nsv899068	chr12:49714103-49924637	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv832405	chr12:49720279-49910862	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49731000-49735800	Weak transcription	Gastric	stomach
2	chr12:49731600-49736000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr12:49732000-49736600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr12:49733400-49735800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
5	chr12:49733400-49736000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr12:49733600-49735800	Weak transcription	Colonic Mucosa	Colon
7	chr12:49733600-49736000	Weak transcription	A549	lung
8	chr12:49733800-49735800	Weak transcription	Duodenum Mucosa	Duodenum
9	chr12:49733800-49736000	Weak transcription	Pancreas	Pancrea
10	chr12:49733800-49736000	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr12:49733800-49736000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr12:49734200-49739400	Weak transcription	Hela-S3	cervix
13	chr12:49734600-49735800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
14	chr12:49734600-49735800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr12:49734800-49736600	Enhancers	Spleen	Spleen
16	chr12:49735000-49735800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
17	chr12:49735000-49735800	Bivalent Enhancer	Fetal Muscle Leg	muscle
18	chr12:49735000-49737000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
19	chr12:49735200-49735800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
20	chr12:49735200-49735800	Weak transcription	K562	blood
21	chr12:49735400-49735800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr12:49735400-49735800	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:49735400-49735800	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr12:49735400-49735800	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr12:49735400-49735800	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
26	chr12:49735400-49735800	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
27	chr12:49735400-49735800	Bivalent Enhancer	Fetal Stomach	stomach
28	chr12:49735400-49736000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr12:49735400-49736000	Flanking Active TSS	Brain Germinal Matrix	brain
30	chr12:49735400-49736200	Bivalent Enhancer	Fetal Intestine Small	intestine
31	chr12:49735400-49736400	Bivalent Enhancer	Primary hematopoietic stem cells	blood
32	chr12:49735400-49736600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
33	chr12:49735400-49736600	Bivalent Enhancer	Fetal Brain Male	brain
34	chr12:49735400-49737000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
35	chr12:49735400-49737000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
36	chr12:49735400-49737200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
37	chr12:49735600-49735800	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:49735600-49735800	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr12:49735600-49735800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
40	chr12:49735600-49735800	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
41	chr12:49735600-49735800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
42	chr12:49735600-49735800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr12:49735600-49735800	Bivalent Enhancer	Stomach Smooth Muscle	stomach
44	chr12:49735600-49735800	Flanking Bivalent TSS/Enh	HepG2	liver
45	chr12:49735600-49735800	Bivalent/Poised TSS	Monocytes-CD14+_RO01746	blood
46	chr12:49735600-49736000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr12:49735600-49736000	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr12:49735600-49736000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr12:49735600-49736000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr12:49735600-49736000	Bivalent/Poised TSS	Fetal Brain Female	brain

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