Variant report

Variant	rs12299391
Chromosome Location	chr12:105628835-105628836
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:105628276-105630777	MCF10A-Er-Src	breast:	n/a	n/a
2	HCFC1	chr12:105628448-105630871	Hela-S3	cervix:	n/a	n/a
3	MYC	chr12:105628673-105629399	MCF10A-Er-Src	breast:	n/a	chr12:105629275-105629284

No data

(count:11 , 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	chr12:105610784..105617210-chr12:105628529..105631630,8	MCF-7	breast:
8	chr12:105501540..105503183-chr12:105627693..105630661,2	MCF-7	breast:
9	chr12:105500023..105502355-chr12:105628064..105629909,2	K562	blood:
10	chr12:105500023..105504653-chr12:105628064..105630551,4	K562	blood:
11	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
ENSG00000136051	Chromatin interaction
ENSG00000257999	Chromatin interaction
ENSG00000136044	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

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	0.81[AMR][1000 genomes];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]
rs12299366	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12301914	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12304384	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12305766	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12307372	0.89[EUR][1000 genomes]
rs12308444	0.84[AFR][1000 genomes];0.93[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	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12317804	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12321199	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12321518	0.94[AFR][1000 genomes];0.96[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	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12424709	0.97[AFR][1000 genomes];0.96[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	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59320697	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59593474	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60835294	0.92[EUR][1000 genomes]
rs60999193	0.89[AFR][1000 genomes];0.96[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	0.96[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	0.86[AFR][1000 genomes];0.96[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]
rs73181860	0.81[AMR][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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