Variant report

Variant	rs9498259
Chromosome Location	chr6:149542795-149542796
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:149535249..149539835-chr6:149540591..149543214,5	K562	blood:
2	chr6:149407215..149409434-chr6:149542169..149544216,2	K562	blood:
3	chr6:149541868..149543777-chr6:149546519..149549131,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TAB2-1	chr6:149541943-149544218	NONHSAT115488

Variant related genes	Relation type
ENSG00000055208	Chromatin interaction
ENSG00000228408	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11965012	1.00[ASN][1000 genomes]
rs11968376	1.00[EUR][1000 genomes]
rs11968394	1.00[EUR][1000 genomes]
rs13437225	1.00[ASN][1000 genomes]
rs3813677	1.00[EUR][1000 genomes]
rs57567299	1.00[EUR][1000 genomes]
rs58764592	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73779098	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73781703	1.00[ASN][1000 genomes]
rs7748133	0.87[ASN][1000 genomes]
rs7748668	1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7748833	1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9485359	1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9498254	1.00[EUR][1000 genomes]
rs9498258	1.00[JPT][hapmap];0.83[YRI][hapmap];1.00[ASN][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:31 , 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	chr6:149534200-149547600	Weak transcription	Primary T cells from cord blood	blood
3	chr6:149534400-149545800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr6:149534800-149548600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr6:149535000-149546800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr6:149538200-149544600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr6:149538200-149548600	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr6:149539400-149544800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr6:149540000-149545200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr6:149540200-149544400	Weak transcription	Fetal Lung	lung
11	chr6:149540400-149544800	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr6:149540400-149551600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr6:149540600-149547200	Weak transcription	Brain Substantia Nigra	brain
14	chr6:149541400-149546600	Weak transcription	Brain Cingulate Gyrus	brain
15	chr6:149541600-149544600	Weak transcription	Brain Hippocampus Middle	brain
16	chr6:149542000-149542800	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr6:149542200-149542800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr6:149542200-149543000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:149542200-149543000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr6:149542200-149543200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr6:149542200-149560600	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr6:149542400-149543000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr6:149542400-149543200	Enhancers	Brain Germinal Matrix	brain
24	chr6:149542400-149543400	Enhancers	HSMMtube	muscle
25	chr6:149542400-149543400	Enhancers	NH-A	brain
26	chr6:149542400-149543400	Enhancers	Osteobl	bone
27	chr6:149542400-149546200	Enhancers	Fetal Heart	heart
28	chr6:149542600-149542800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:149542600-149542800	Enhancers	Brain Anterior Caudate	brain
30	chr6:149542600-149543600	Enhancers	HSMM	muscle
31	chr6:149542600-149546000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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