Variant report

Variant	rs12299777
Chromosome Location	chr12:49735181-49735182
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:61)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

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	chr12:49735080-49735230	Hela-S3	cervix:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:49735181-49735231	HNPCEpiC	eye:	n/a
2	chr12:49735181-49735231	GM12892	blood:	n/a
3	chr12:49735181-49735231	MCF10A-Er-Src	breast:	n/a
4	chr12:49735181-49735231	AG04450	lung:	fetal
5	chr12:49735181-49735231	NHDF-neo	bronchial:	n/a
6	chr12:49735181-49735231	HCT-116	colon:	n/a
7	chr12:49735181-49735231	AG09319	gingival:	n/a
8	chr12:49735181-49735231	HEEpiC	esophagus:	n/a
9	chr12:49735181-49735231	CMK	blood:	n/a
10	chr12:49735181-49735231	U87	brain:	n/a
11	chr12:49735181-49735231	HL-60	blood:	n/a
12	chr12:49735181-49735231	SK-N-SH	brain:	n/a
13	chr12:49735181-49735231	LNCaP	prostate:	n/a
14	chr12:49735181-49735231	ovcar-3	ovarian:	n/a
15	chr12:49735181-49735231	HEK293	kidney:	embryo
16	chr12:49735181-49735231	HUVEC	blood vessel:	n/a
17	chr12:49735181-49735231	HPAEpiC	pulmonary alveolar:	n/a
18	chr12:49735181-49735231	HepG2	liver:	n/a
19	chr12:49735181-49735231	BE2_C	brain:	n/a
20	chr12:49735181-49735231	NHBE	bronchial:	n/a
21	chr12:49735181-49735231	HAEpiC	amniotic membrane:	n/a
22	chr12:49735181-49735231	IMR90	lung:	fetal
23	chr12:49735181-49735231	H1-hESC	embryonic stem cell:	embryo
24	chr12:49735181-49735231	K562	blood:	n/a
25	chr12:49735181-49735231	AG09309	skin:	n/a
26	chr12:49735181-49735231	SKMC	muscle:	n/a
27	chr12:49735181-49735231	T-47D	breast:	n/a
28	chr12:49735181-49735231	NH-A	brain:	n/a
29	chr12:49735181-49735231	AG10803	skin:	n/a
30	chr12:49735181-49735231	HCPEpiC	choroid plexus:	n/a
31	chr12:49735181-49735231	HCF	heart:	n/a
32	chr12:49735181-49735231	ECC-1	luminal epithelium:	n/a
33	chr12:49735181-49735231	Hela-S3	cervix:	n/a
34	chr12:49735181-49735231	A549	lung:	n/a
35	chr12:49735181-49735231	Jurkat	blood:	n/a
36	chr12:49735181-49735231	GM06990	blood:	n/a
37	chr12:49735181-49735231	MCF-7	breast:	n/a
38	chr12:49735181-49735231	PANC-1	pancreas:	n/a
39	chr12:49735181-49735231	SK-N-MC	brain:	n/a
40	chr12:49735181-49735231	NB4	blood:	n/a
41	chr12:49735181-49735231	GM19239	blood:	n/a
42	chr12:49735181-49735231	AG04449	skin:	fetal
43	chr12:49735181-49735231	ProgFib	skin:	n/a
44	chr12:49735181-49735231	GM12891	blood:	n/a
45	chr12:49735181-49735231	PFSK-1	brain:	n/a
46	chr12:49735181-49735231	GM12878	blood:	n/a
47	chr12:49735181-49735231	RPTEC	kidney:	n/a
48	chr12:49735181-49735231	NT2-D1	testis:	n/a
49	chr12:49735181-49735231	SAEC	small airway:	n/a
50	chr12:49735181-49735231	AoSMC	blood vessel:	n/a

(count:10 , 50 per page) page: 1

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	chr12:49720134..49722975-chr12:49734541..49736256,2	MCF-7	breast:
5	chr12:49667825..49672911-chr12:49731373..49736764,7	K562	blood:
6	chr12:49655321..49661148-chr12:49729487..49743115,26	K562	blood:
7	chr12:49685452..49688091-chr12:49734714..49737225,2	MCF-7	breast:
8	chr12:49735114..49738057-chr12:49759505..49762701,3	K562	blood:
9	chr12:49666079..49671115-chr12:49733959..49736436,6	K562	blood:
10	chr12:49665205..49667144-chr12:49734147..49736854,2	MCF-7	breast:

No data

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

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10506285	0.81[ASN][1000 genomes]
rs11168981	0.94[ASN][1000 genomes]
rs11831313	0.81[ASN][1000 genomes]
rs12306866	0.94[ASN][1000 genomes]
rs12310129	0.81[ASN][1000 genomes]
rs12317856	0.81[ASN][1000 genomes]
rs17123696	0.81[ASN][1000 genomes]
rs1874909	0.87[ASN][1000 genomes]
rs1874910	0.87[ASN][1000 genomes]
rs1874911	0.87[ASN][1000 genomes]
rs2270741	0.87[ASN][1000 genomes]
rs60331259	0.81[ASN][1000 genomes]
rs60494978	0.81[ASN][1000 genomes]
rs74089059	0.94[ASN][1000 genomes]
rs74089062	0.87[ASN][1000 genomes]
rs7955245	0.81[ASN][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:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49731000-49735800	Weak transcription	Gastric	stomach
2	chr12:49731400-49735200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
3	chr12:49731400-49735600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr12:49731600-49735200	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
5	chr12:49731600-49736000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr12:49732000-49735400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:49732000-49736600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr12:49733000-49735200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
9	chr12:49733200-49735400	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
10	chr12:49733400-49735400	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:49733400-49735800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
12	chr12:49733400-49736000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr12:49733600-49735800	Weak transcription	Colonic Mucosa	Colon
14	chr12:49733600-49736000	Weak transcription	A549	lung
15	chr12:49733800-49735400	Enhancers	Brain Germinal Matrix	brain
16	chr12:49733800-49735800	Weak transcription	Duodenum Mucosa	Duodenum
17	chr12:49733800-49736000	Weak transcription	Pancreas	Pancrea
18	chr12:49733800-49736000	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr12:49733800-49736000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr12:49734000-49735200	Enhancers	K562	blood
21	chr12:49734200-49735200	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
22	chr12:49734200-49735600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr12:49734200-49739400	Weak transcription	Hela-S3	cervix
24	chr12:49734400-49735600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:49734600-49735400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
26	chr12:49734600-49735400	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr12:49734600-49735600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr12:49734600-49735800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
29	chr12:49734600-49735800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr12:49734800-49735400	Enhancers	HSMMtube	muscle
31	chr12:49734800-49736600	Enhancers	Spleen	Spleen
32	chr12:49735000-49735200	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr12:49735000-49735200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr12:49735000-49735200	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
35	chr12:49735000-49735600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
36	chr12:49735000-49735800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
37	chr12:49735000-49735800	Bivalent Enhancer	Fetal Muscle Leg	muscle
38	chr12:49735000-49737000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell

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