Variant report

Variant	rs12206090
Chromosome Location	chr6:149548902-149548903
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:149541868..149543777-chr6:149546519..149549131,2	K562	blood:
2	chr6:149351744..149354511-chr6:149547330..149549767,2	MCF-7	breast:
3	chr6:149545459..149547626-chr6:149547997..149549609,2	K562	blood:
4	chr6:149548430..149549948-chr6:149553573..149556113,2	MCF-7	breast:
5	chr6:149546460..149549021-chr6:149637150..149639241,2	MCF-7	breast:
6	chr6:149547500..149550103-chr6:149637662..149639707,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000055208	Chromatin interaction
ENSG00000236591	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11965012	0.90[EUR][1000 genomes]
rs12197526	0.90[EUR][1000 genomes]
rs12197595	0.90[EUR][1000 genomes]
rs12200718	0.90[EUR][1000 genomes]
rs12201953	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12201961	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12202447	0.90[EUR][1000 genomes]
rs12202776	0.82[EUR][1000 genomes]
rs12203964	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12207651	0.93[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12211226	0.82[EUR][1000 genomes]
rs12213399	0.90[EUR][1000 genomes]
rs12215601	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes]
rs13437225	0.90[EUR][1000 genomes]
rs60916218	0.93[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs73781703	0.90[EUR][1000 genomes]
rs73781705	0.93[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs73781708	0.93[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs73781709	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73781711	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73781712	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73781713	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9498253	0.90[EUR][1000 genomes]
rs9498254	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9498258	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032319	chr6:149271433-149550525	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv538470	chr6:149271433-149550525	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1024776	chr6:149398652-149654593	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers 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:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149533200-149549400	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr6:149540400-149551600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr6:149542200-149560600	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr6:149544400-149549600	Enhancers	Fetal Lung	lung
5	chr6:149545400-149550400	Weak transcription	Right Ventricle	heart
6	chr6:149545400-149553000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr6:149545600-149549600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:149545800-149549400	Weak transcription	HSMM	muscle
9	chr6:149545800-149551600	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr6:149545800-149553000	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr6:149545800-149557800	Weak transcription	Colon Smooth Muscle	Colon
12	chr6:149545800-149560200	Weak transcription	Right Atrium	heart
13	chr6:149546000-149551600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr6:149546200-149549000	Weak transcription	Fetal Heart	heart
15	chr6:149546800-149556200	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr6:149547200-149549400	Enhancers	Brain Substantia Nigra	brain
17	chr6:149547400-149549400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr6:149547600-149549000	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr6:149547600-149549000	Weak transcription	Fetal Brain Male	brain
20	chr6:149547600-149549600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr6:149547600-149550000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr6:149547800-149549400	Weak transcription	Brain Anterior Caudate	brain
23	chr6:149548000-149549000	Weak transcription	Brain Hippocampus Middle	brain
24	chr6:149548000-149549400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr6:149548000-149551400	Weak transcription	Adipose Nuclei	Adipose
26	chr6:149548400-149549400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:149548600-149549400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr6:149548600-149550000	Enhancers	HUES64 Cell Line	embryonic stem cell
29	chr6:149548600-149550200	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr6:149548600-149551000	Enhancers	Brain Germinal Matrix	brain
31	chr6:149548800-149549200	Weak transcription	Brain Cingulate Gyrus	brain
32	chr6:149548800-149549200	Weak transcription	Ovary	ovary
33	chr6:149548800-149549400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr6:149548800-149549400	Weak transcription	Fetal Stomach	stomach
35	chr6:149548800-149549400	Weak transcription	Fetal Thymus	thymus
36	chr6:149548800-149549400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr6:149548800-149551000	Enhancers	Fetal Brain Female	brain

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