Variant report

Variant	rs9498253
Chromosome Location	chr6:149535085-149535086
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	USF2	chr6:149534769-149535219	GM12878	blood:	n/a	n/a
2	CEBPB	chr6:149535085-149535282	A549	lung:	n/a	n/a
3	BCL3	chr6:149534977-149535431	GM12878	blood:	n/a	n/a
4	TEAD4	chr6:149534937-149535325	K562	blood:	n/a	n/a
5	RCOR1	chr6:149534825-149535255	K562	blood:	n/a	n/a
6	CEBPB	chr6:149534979-149535404	IMR90	lung:	n/a	n/a
7	RUNX3	chr6:149533795-149535358	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:149532501..149535186-chr6:149537536..149540532,2	MCF-7	breast:
2	chr6:149529664..149531890-chr6:149533306..149535145,2	K562	blood:

Variant related genes	Relation type
TAB2	TF binding region
ENSG00000228408	TF binding region
ENSG00000055208	Chromatin interaction
ENSG00000228408	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11965012	0.90[EUR][1000 genomes]
rs12197526	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12197595	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12200718	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12201953	0.90[EUR][1000 genomes]
rs12201961	0.90[EUR][1000 genomes]
rs12202447	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12202776	0.81[EUR][1000 genomes]
rs12203964	0.85[EUR][1000 genomes]
rs12206090	0.90[EUR][1000 genomes]
rs12207651	0.90[EUR][1000 genomes]
rs12211226	0.81[EUR][1000 genomes]
rs12213399	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13437225	0.90[EUR][1000 genomes]
rs60916218	0.90[EUR][1000 genomes]
rs73781703	0.90[EUR][1000 genomes]
rs73781705	0.90[EUR][1000 genomes]
rs73781708	0.90[EUR][1000 genomes]
rs73781709	0.90[EUR][1000 genomes]
rs73781711	0.85[EUR][1000 genomes]
rs73781712	0.85[EUR][1000 genomes]
rs73781713	0.85[EUR][1000 genomes]
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:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:149530600-149535400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr6:149530600-149535400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr6:149530600-149535600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr6:149530600-149535600	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr6:149530800-149535400	Enhancers	Fetal Heart	heart
6	chr6:149530800-149535400	Enhancers	Fetal Lung	lung
7	chr6:149530800-149535600	Enhancers	Primary hematopoietic stem cells	blood
8	chr6:149530800-149535600	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr6:149530800-149535600	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr6:149530800-149535600	Enhancers	Fetal Stomach	stomach
11	chr6:149530800-149536000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr6:149531000-149535200	Enhancers	Osteobl	bone
13	chr6:149531000-149535400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr6:149533200-149549400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr6:149533400-149535200	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr6:149533600-149535600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr6:149533800-149535800	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr6:149534000-149537000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr6:149534200-149535400	Enhancers	Muscle Satellite Cultured Cells	--
20	chr6:149534200-149547600	Weak transcription	Primary T cells from cord blood	blood
21	chr6:149534400-149535400	Enhancers	Brain Hippocampus Middle	brain
22	chr6:149534400-149545800	Weak transcription	Stomach Smooth Muscle	stomach
23	chr6:149534600-149535200	Weak transcription	HMEC	breast
24	chr6:149534600-149535600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr6:149534600-149535800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr6:149534600-149536000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr6:149534600-149538800	Weak transcription	Brain Cingulate Gyrus	brain
28	chr6:149534600-149539000	Weak transcription	Colon Smooth Muscle	Colon
29	chr6:149534800-149536800	Weak transcription	Fetal Thymus	thymus
30	chr6:149534800-149537600	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr6:149534800-149538600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr6:149534800-149542200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr6:149534800-149542200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr6:149534800-149548600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr6:149535000-149535200	Enhancers	GM12878-XiMat	blood
36	chr6:149535000-149535200	Enhancers	HSMM	muscle
37	chr6:149535000-149537800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr6:149535000-149538800	Weak transcription	Brain Substantia Nigra	brain
39	chr6:149535000-149542600	Weak transcription	Brain Anterior Caudate	brain
40	chr6:149535000-149546800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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