Variant report

Variant	rs853680
Chromosome Location	chr6:28296846-28296847
allele	C/G
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	chr6:28296430-28296932	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:28104111..28106206-chr6:28296771..28301344,4	K562	blood:
2	chr6:28235190..28237115-chr6:28295999..28298391,2	K562	blood:
3	chr6:28103055..28111556-chr6:28296771..28308203,17	K562	blood:
4	chr6:28277054..28279277-chr6:28294657..28297286,2	K562	blood:

Variant related genes	Relation type
ZSCAN31	TF binding region
ENSG00000269293	Chromatin interaction
ENSG00000261839	Chromatin interaction
ENSG00000198315	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1144707	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1150667	1.00[AMR][1000 genomes]
rs1150675	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1150677	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1150681	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1150706	1.00[AMR][1000 genomes]
rs12208060	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1225589	1.00[AMR][1000 genomes]
rs1225601	1.00[AMR][1000 genomes]
rs1233663	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1233668	1.00[AMR][1000 genomes]
rs1778485	1.00[AMR][1000 genomes]
rs213229	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs213234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs213242	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2394048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2531829	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2743874	1.00[YRI][hapmap]
rs2799080	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2859357	1.00[YRI][hapmap]
rs2859361	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs2859366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4713154	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59183152	1.00[AMR][1000 genomes]
rs853675	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs853677	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs853686	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs853691	1.00[AMR][1000 genomes]
rs853692	1.00[YRI][hapmap];1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28288200-28299200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr6:28290800-28298200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
3	chr6:28291400-28298000	ZNF genes & repeats	Liver	Liver
4	chr6:28292600-28297200	ZNF genes & repeats	Stomach Smooth Muscle	stomach
5	chr6:28294800-28302000	Weak transcription	HepG2	liver
6	chr6:28294800-28302800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr6:28295400-28297000	Strong transcription	Fetal Muscle Trunk	muscle
8	chr6:28295400-28301400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr6:28295400-28302400	Weak transcription	Brain Angular Gyrus	brain
10	chr6:28295400-28302800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr6:28295400-28303000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr6:28295400-28303000	Weak transcription	Thymus	Thymus
13	chr6:28295600-28297000	Weak transcription	Brain Anterior Caudate	brain
14	chr6:28295600-28297000	Weak transcription	Duodenum Mucosa	Duodenum
15	chr6:28295600-28297200	Weak transcription	Fetal Brain Female	brain
16	chr6:28295600-28297800	Weak transcription	K562	blood
17	chr6:28295600-28302000	Weak transcription	Fetal Heart	heart
18	chr6:28295600-28302200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr6:28295600-28302200	Weak transcription	Hela-S3	cervix
20	chr6:28295600-28302400	Weak transcription	Brain Substantia Nigra	brain
21	chr6:28295600-28302600	Weak transcription	Stomach Mucosa	stomach
22	chr6:28295600-28302800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr6:28295600-28302800	Weak transcription	Fetal Brain Male	brain
24	chr6:28295800-28302800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr6:28296400-28297400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr6:28296400-28297400	Strong transcription	Left Ventricle	heart
27	chr6:28296600-28297000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr6:28296600-28297000	ZNF genes & repeats	Colonic Mucosa	Colon
29	chr6:28296600-28297200	ZNF genes & repeats	Pancreas	Pancrea
30	chr6:28296600-28297400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
31	chr6:28296600-28297400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
32	chr6:28296600-28297400	ZNF genes & repeats	Colon Smooth Muscle	Colon
33	chr6:28296600-28297400	ZNF genes & repeats	Fetal Intestine Large	intestine
34	chr6:28296600-28297400	ZNF genes & repeats	Fetal Intestine Small	intestine
35	chr6:28296600-28297400	ZNF genes & repeats	Fetal Stomach	stomach
36	chr6:28296600-28297400	ZNF genes & repeats	Ovary	ovary
37	chr6:28296600-28297600	ZNF genes & repeats	Fetal Muscle Leg	muscle
38	chr6:28296600-28298200	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
39	chr6:28296800-28297000	ZNF genes & repeats	Brain Germinal Matrix	brain
40	chr6:28296800-28297000	ZNF genes & repeats	Gastric	stomach
41	chr6:28296800-28297200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr6:28296800-28297200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
43	chr6:28296800-28297200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr6:28296800-28297200	ZNF genes & repeats	Adipose Nuclei	Adipose
45	chr6:28296800-28297200	Strong transcription	Brain Cingulate Gyrus	brain
46	chr6:28296800-28297200	ZNF genes & repeats	Brain Hippocampus Middle	brain
47	chr6:28296800-28297200	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
48	chr6:28296800-28297200	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
49	chr6:28296800-28297200	ZNF genes & repeats	Right Ventricle	heart
50	chr6:28296800-28297200	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle

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