Variant report

Variant	rs11968339
Chromosome Location	chr6:24802617-24802618
allele	C/T
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	POLR2A	chr6:24802580-24802848	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:24794462..24796300-chr6:24800583..24803323,2	K562	blood:

Variant related genes	Relation type
C6orf229	TF binding region

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12333181	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6932270	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7356830	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9295633	1.00[AMR][1000 genomes]
rs9467307	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9467310	0.88[AFR][1000 genomes]
rs9467313	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9467315	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830609	chr6:24712086-24896647	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv5227	chr6:24774149-24824012	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv508396	chr6:24779648-24846309	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24776400-24803200	Weak transcription	HSMMtube	muscle
2	chr6:24776400-24807400	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr6:24776800-24807600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr6:24777000-24805000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr6:24777000-24806200	Weak transcription	Spleen	Spleen
6	chr6:24777000-24808000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr6:24777000-24809400	Weak transcription	Brain Germinal Matrix	brain
8	chr6:24777000-24811600	Weak transcription	Brain Hippocampus Middle	brain
9	chr6:24777000-24847600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr6:24777000-24859600	Weak transcription	Psoas Muscle	Psoas
11	chr6:24782400-24803000	Weak transcription	Pancreas	Pancrea
12	chr6:24787600-24806200	Weak transcription	Fetal Stomach	stomach
13	chr6:24788000-24805600	Weak transcription	Fetal Muscle Leg	muscle
14	chr6:24788000-24810200	Weak transcription	Left Ventricle	heart
15	chr6:24788000-24832000	Weak transcription	Brain Substantia Nigra	brain
16	chr6:24788800-24848200	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr6:24789000-24807000	Weak transcription	GM12878-XiMat	blood
18	chr6:24789200-24805800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr6:24789200-24807400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr6:24789200-24842600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr6:24789400-24807400	Weak transcription	Fetal Muscle Trunk	muscle
22	chr6:24789400-24807800	Weak transcription	Dnd41	blood
23	chr6:24798200-24827400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr6:24798200-24841200	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr6:24799400-24805000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr6:24799400-24805000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr6:24800000-24807400	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr6:24800000-24843200	Weak transcription	Liver	Liver
29	chr6:24800200-24806600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr6:24800200-24809400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr6:24800400-24803000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr6:24800400-24821800	Weak transcription	Fetal Heart	heart
33	chr6:24800600-24806200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr6:24800800-24811800	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr6:24800800-24811800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr6:24801000-24812000	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr6:24801200-24811800	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr6:24801200-24812000	Strong transcription	Primary B cells from peripheral blood	blood
39	chr6:24801400-24811800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr6:24801600-24811200	Strong transcription	Primary T cells from cord blood	blood
41	chr6:24802000-24803600	Enhancers	NHDF-Ad	bronchial
42	chr6:24802000-24806400	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr6:24802000-24810600	Strong transcription	Primary B cells from cord blood	blood
44	chr6:24802000-24811000	Strong transcription	Primary hematopoietic stem cells	blood
45	chr6:24802000-24811000	Strong transcription	Fetal Thymus	thymus
46	chr6:24802000-24811600	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr6:24802000-24811800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr6:24802000-24811800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr6:24802000-24812000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr6:24802200-24803000	Enhancers	HepG2	liver

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