Variant report

Variant	rs11068003
Chromosome Location	chr12:116797470-116797471
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:116795827..116800333-chr12:116800677..116806622,10	K562	blood:
2	chr12:116794823..116797570-chr12:116823877..116825448,2	K562	blood:
3	chr12:116728521..116730114-chr12:116796783..116799180,2	MCF-7	breast:
4	chr12:116795827..116800092-chr12:116804104..116806622,3	K562	blood:
5	chr12:116713317..116716868-chr12:116795567..116799034,4	MCF-7	breast:
6	chr12:116796080..116800323-chr12:116810263..116814376,4	K562	blood:
7	chr12:116712861..116715837-chr12:116795906..116798539,2	K562	blood:
8	chr12:116796063..116798440-chr12:116800677..116803897,4	K562	blood:
9	chr12:116782797..116785324-chr12:116796458..116799229,3	K562	blood:
10	chr12:116714337..116716286-chr12:116794773..116798539,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000258346	Chromatin interaction
ENSG00000123066	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10850618	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs10850619	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs11068006	1.00[ASW][hapmap];0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.87[MKK][hapmap];0.88[TSI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11068007	0.90[CEU][hapmap];0.81[CHB][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12228903	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12230486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12371905	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17615178	1.00[LWK][hapmap]
rs57615867	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11068003	SLC24A6	cis	cerebellum	SCAN
rs11068003	NAA25	cis	parietal	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:116795200-116800000	Enhancers	Fetal Muscle Trunk	muscle
2	chr12:116795400-116800000	Enhancers	Fetal Muscle Leg	muscle
3	chr12:116795600-116798800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:116795800-116798000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr12:116796000-116797800	Enhancers	Fetal Heart	heart
6	chr12:116796200-116797800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr12:116796200-116798000	Enhancers	Fetal Intestine Small	intestine
8	chr12:116796400-116797600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr12:116796400-116797600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr12:116796400-116797600	Enhancers	Colon Smooth Muscle	Colon
11	chr12:116796400-116797600	Flanking Active TSS	GM12878-XiMat	blood
12	chr12:116796400-116797800	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr12:116796400-116797800	Enhancers	Duodenum Smooth Muscle	Duodenum
14	chr12:116796400-116798600	Enhancers	Fetal Intestine Large	intestine
15	chr12:116796400-116799600	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr12:116796400-116799600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr12:116796600-116797600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr12:116796600-116797600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr12:116796600-116797600	Enhancers	Stomach Mucosa	stomach
20	chr12:116796600-116797600	Enhancers	HMEC	breast
21	chr12:116796600-116797600	Flanking Active TSS	NHEK	skin
22	chr12:116796600-116797600	Flanking Active TSS	Osteobl	bone
23	chr12:116796600-116797800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr12:116796600-116797800	Flanking Active TSS	Dnd41	blood
25	chr12:116796600-116797800	Enhancers	HSMMtube	muscle
26	chr12:116796600-116798000	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr12:116796600-116798000	Enhancers	Placenta	Placenta
28	chr12:116796600-116800000	Enhancers	Primary hematopoietic stem cells	blood
29	chr12:116796800-116797600	Flanking Active TSS	Primary B cells from cord blood	blood
30	chr12:116796800-116797600	Flanking Active TSS	Primary B cells from peripheral blood	blood
31	chr12:116796800-116797600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr12:116796800-116797600	Enhancers	Placenta Amnion	Placenta Amnion
33	chr12:116796800-116797800	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr12:116796800-116798400	Weak transcription	Psoas Muscle	Psoas
35	chr12:116796800-116798800	Weak transcription	Spleen	Spleen
36	chr12:116796800-116803800	Weak transcription	Colonic Mucosa	Colon
37	chr12:116797000-116797600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:116797000-116797600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr12:116797000-116797600	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr12:116797000-116797600	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr12:116797000-116797600	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr12:116797000-116797600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr12:116797000-116797600	Enhancers	Brain Hippocampus Middle	brain
44	chr12:116797000-116797600	Enhancers	Brain Substantia Nigra	brain
45	chr12:116797000-116797600	Enhancers	Fetal Brain Female	brain
46	chr12:116797000-116797600	Enhancers	Fetal Kidney	kidney
47	chr12:116797000-116797600	Enhancers	Right Atrium	heart
48	chr12:116797000-116797600	Enhancers	NHLF	lung
49	chr12:116797000-116797800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr12:116797000-116797800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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