Variant report

Variant	rs12299366
Chromosome Location	chr12:105628919-105628920
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:105628893-105630852	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr12:105628276-105630777	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr12:105628888-105630747	MCF10A-Er-Src	breast:	n/a	n/a
4	HCFC1	chr12:105628448-105630871	Hela-S3	cervix:	n/a	n/a
5	MYC	chr12:105628673-105629399	MCF10A-Er-Src	breast:	n/a	chr12:105629275-105629284
6	POLR2A	chr12:105628872-105630468	HUVEC	blood vessel:	n/a	n/a
7	MXI1	chr12:105628916-105630642	IMR90	lung:	n/a	chr12:105630122-105630137
8	FOXA1	chr12:105628850-105629198	HepG2	liver:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:105606795..105619301-chr12:105624368..105633184,26	MCF-7	breast:
2	chr12:105628750..105631438-chr12:105722608..105725285,3	MCF-7	breast:
3	chr12:105599435..105602379-chr12:105626303..105628956,2	K562	blood:
4	chr12:105620755..105625323-chr12:105625745..105629848,5	K562	blood:
5	chr12:105609511..105612358-chr12:105625566..105629291,3	K562	blood:
6	chr12:105499144..105502991-chr12:105627617..105631044,5	MCF-7	breast:
7	chr12:105628899..105630525-chr15:65596241..65598833,2	MCF-7	breast:
8	chr12:105610784..105617210-chr12:105628529..105631630,8	MCF-7	breast:
9	chr12:105501540..105503183-chr12:105627693..105630661,2	MCF-7	breast:
10	chr12:105500023..105502355-chr12:105628064..105629909,2	K562	blood:
11	chr12:105500023..105504653-chr12:105628064..105630551,4	K562	blood:
12	chr12:105542946..105545712-chr12:105628511..105631314,2	MCF-7	breast:

No data

Variant related genes	Relation type
APPL2	TF binding region
C12orf75	TF binding region
ENSG00000235162	Chromatin interaction
ENSG00000257999	Chromatin interaction
ENSG00000136051	Chromatin interaction
ENSG00000200156	Chromatin interaction
ENSG00000136044	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10083185	0.92[EUR][1000 genomes]
rs10161513	1.00[ASN][1000 genomes]
rs11112381	0.92[EUR][1000 genomes]
rs11112389	0.91[EUR][1000 genomes]
rs11112410	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11112452	1.00[ASN][1000 genomes]
rs11112522	1.00[ASN][1000 genomes]
rs11112526	1.00[ASN][1000 genomes]
rs11559871	0.86[EUR][1000 genomes]
rs11829598	0.92[EUR][1000 genomes]
rs12299391	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12301914	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12304384	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12305766	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12307372	0.89[EUR][1000 genomes]
rs12308444	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12311156	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12312965	0.92[EUR][1000 genomes]
rs12317637	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12317804	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12321199	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12321518	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12321534	0.83[EUR][1000 genomes]
rs12424095	1.00[ASN][1000 genomes]
rs12424191	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12424709	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12425803	0.92[EUR][1000 genomes]
rs17037098	1.00[ASN][1000 genomes]
rs56284118	0.92[EUR][1000 genomes]
rs56862143	0.92[EUR][1000 genomes]
rs58780154	1.00[ASN][1000 genomes]
rs59320697	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59593474	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60835294	0.92[EUR][1000 genomes]
rs60999193	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7132816	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7133728	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7136453	0.92[EUR][1000 genomes]
rs7138574	0.89[EUR][1000 genomes]
rs7300130	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7302842	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7305406	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7306679	1.00[ASN][1000 genomes]
rs7313309	0.92[EUR][1000 genomes]
rs7315964	0.92[EUR][1000 genomes]
rs73179990	0.92[EUR][1000 genomes]
rs73179996	0.92[EUR][1000 genomes]
rs73179998	0.92[EUR][1000 genomes]
rs73180001	0.92[EUR][1000 genomes]
rs73181810	1.00[ASN][1000 genomes]
rs73181818	1.00[ASN][1000 genomes]
rs73181822	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73181825	1.00[ASN][1000 genomes]
rs73181843	1.00[ASN][1000 genomes]
rs73181852	1.00[ASN][1000 genomes]
rs73181856	1.00[ASN][1000 genomes]
rs73181857	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73181869	1.00[ASN][1000 genomes]
rs7964184	0.92[EUR][1000 genomes]
rs7971630	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975115	1.00[ASN][1000 genomes]
rs7975787	0.89[EUR][1000 genomes]
rs7978034	0.92[EUR][1000 genomes]

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	nsv832506	chr12:105461274-105637561	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	nsv455704	chr12:105583877-105651356	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
3	nsv560053	chr12:105583877-105651356	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
4	nsv899499	chr12:105616297-105722529	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105616600-105629000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:105617000-105629000	Weak transcription	Esophagus	oesophagus
3	chr12:105617400-105629000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:105622000-105629000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:105625600-105629000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr12:105625600-105629000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr12:105626400-105629400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr12:105626600-105629000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr12:105626600-105629200	Flanking Active TSS	Fetal Brain Female	brain
10	chr12:105626800-105629000	Flanking Active TSS	Brain Anterior Caudate	brain
11	chr12:105626800-105629000	Enhancers	Small Intestine	intestine
12	chr12:105627000-105629000	Weak transcription	Lung	lung
13	chr12:105627000-105629400	Flanking Active TSS	Primary T cells from cord blood	blood
14	chr12:105627200-105629000	Weak transcription	Gastric	stomach
15	chr12:105627200-105629000	Weak transcription	Pancreas	Pancrea
16	chr12:105627600-105629000	Flanking Active TSS	Brain Substantia Nigra	brain
17	chr12:105627600-105629200	Flanking Active TSS	Duodenum Mucosa	Duodenum
18	chr12:105627600-105629400	Flanking Active TSS	Adipose Nuclei	Adipose
19	chr12:105627600-105630600	Active TSS	Aorta	Aorta
20	chr12:105627800-105629000	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr12:105627800-105629000	Enhancers	Fetal Thymus	thymus
22	chr12:105627800-105629000	Enhancers	Spleen	Spleen
23	chr12:105627800-105629400	Flanking Active TSS	HUVEC	blood vessel
24	chr12:105627800-105629600	Flanking Active TSS	Primary hematopoietic stem cells	blood
25	chr12:105628000-105629000	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:105628000-105629000	Flanking Active TSS	Fetal Lung	lung
27	chr12:105628000-105629200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr12:105628000-105629200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr12:105628000-105629200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
30	chr12:105628000-105629400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
31	chr12:105628000-105629400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
32	chr12:105628000-105629400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
33	chr12:105628000-105629400	Flanking Active TSS	Fetal Kidney	kidney
34	chr12:105628000-105629400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
35	chr12:105628000-105629400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
36	chr12:105628000-105629400	Flanking Active TSS	Dnd41	blood
37	chr12:105628000-105630400	Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr12:105628000-105630600	Active TSS	Colonic Mucosa	Colon
39	chr12:105628200-105629000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr12:105628200-105629000	Flanking Active TSS	Colon Smooth Muscle	Colon
41	chr12:105628200-105629000	Flanking Active TSS	Fetal Heart	heart
42	chr12:105628200-105629000	Flanking Active TSS	A549	lung
43	chr12:105628200-105629200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
44	chr12:105628200-105629200	Flanking Active TSS	HMEC	breast
45	chr12:105628200-105629400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
46	chr12:105628200-105629400	Flanking Active TSS	Fetal Muscle Leg	muscle
47	chr12:105628200-105629600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
48	chr12:105628200-105629600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr12:105628200-105629600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr12:105628200-105629600	Flanking Active TSS	Liver	Liver

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