Variant report

Variant	rs12200717
Chromosome Location	chr6:11112438-11112439
allele	A/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	GATA1	chr6:11111276-11112624	K562	blood:	n/a	n/a
2	GATA2	chr6:11111990-11112502	HUVEC	blood vessel:	n/a	chr6:11112238-11112252
3	CEBPB	chr6:11112438-11112666	K562	blood:	n/a	n/a
4	KAP1	chr6:11111981-11112476	U2OS	brain:	n/a	n/a
5	GATA3	chr6:11111929-11112460	MCF-7	breast:	n/a	n/a
6	GATA3	chr6:11111962-11112473	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr6:11112143-11112438	HUVEC	blood vessel:	n/a	n/a
8	ELF1	chr6:11111868-11112458	K562	blood:	n/a	n/a
9	PML	chr6:11111880-11112558	K562	blood:	n/a	n/a
10	GABPA	chr6:11112099-11112507	HL-60	blood:	n/a	n/a
11	MYC	chr6:11111633-11112620	K562	blood:	n/a	chr6:11112088-11112098
12	JUND	chr6:11111805-11112514	K562	blood:	n/a	n/a
13	TEAD4	chr6:11111552-11112592	K562	blood:	n/a	n/a
14	MAZ	chr6:11111631-11112452	K562	blood:	n/a	n/a
15	EP300	chr6:11111825-11112625	K562	blood:	n/a	n/a
16	ZNF384	chr6:11111789-11112663	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:11092829..11095210-chr6:11111953..11113686,2	K562	blood:

Variant related genes	Relation type
ERVFRD-1	TF binding region
ENSG00000224531	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10484446	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10484448	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10946967	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10946968	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10947002	0.81[ASN][1000 genomes]
rs11751998	0.81[ASN][1000 genomes]
rs11759939	0.90[ASN][1000 genomes]
rs12190970	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12193702	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12194681	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12199551	0.81[ASN][1000 genomes]
rs12200932	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12205389	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211539	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12212683	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12213689	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12215910	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711180	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6456846	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021078	chr6:10819083-11558560	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv538135	chr6:10819083-11558560	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11095200-11122000	Weak transcription	Ovary	ovary
2	chr6:11095600-11135200	Weak transcription	Primary B cells from cord blood	blood
3	chr6:11096600-11120600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr6:11096800-11115000	Weak transcription	NHEK	skin
5	chr6:11096800-11116600	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr6:11096800-11127200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr6:11100800-11116400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:11101600-11134800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr6:11103200-11127000	Weak transcription	Esophagus	oesophagus
10	chr6:11104800-11119400	Weak transcription	Hela-S3	cervix
11	chr6:11107200-11116400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr6:11108400-11113000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr6:11108400-11115400	Weak transcription	GM12878-XiMat	blood
14	chr6:11109000-11116400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr6:11111000-11112600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr6:11111200-11112600	Enhancers	Left Ventricle	heart
17	chr6:11111200-11115000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:11111400-11113000	Enhancers	Adipose Nuclei	Adipose
19	chr6:11111600-11112600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr6:11111600-11112600	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr6:11111600-11112600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr6:11111600-11112600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr6:11111600-11112600	Enhancers	Gastric	stomach
24	chr6:11111600-11112600	Flanking Active TSS	K562	blood
25	chr6:11111600-11112800	Enhancers	HUVEC	blood vessel
26	chr6:11111600-11113000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr6:11111800-11112600	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr6:11111800-11112600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr6:11111800-11113000	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr6:11111800-11115200	Weak transcription	A549	lung
31	chr6:11111800-11120400	Weak transcription	Brain Anterior Caudate	brain
32	chr6:11112000-11112600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
33	chr6:11112000-11112600	Enhancers	Lung	lung
34	chr6:11112000-11112800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr6:11112000-11120400	Weak transcription	Psoas Muscle	Psoas
36	chr6:11112000-11120600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr6:11112200-11112600	Enhancers	Primary T cells fromperipheralblood	blood
38	chr6:11112200-11112600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr6:11112200-11112600	Enhancers	Dnd41	blood
40	chr6:11112200-11112800	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr6:11112200-11112800	Enhancers	Placenta	Placenta
42	chr6:11112200-11112800	Enhancers	HepG2	liver
43	chr6:11112200-11116600	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr6:11112200-11120400	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr6:11112200-11121800	Weak transcription	Fetal Heart	heart
46	chr6:11112400-11112600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr6:11112400-11112600	Enhancers	Primary T helper cells PMA-I stimulated	--
48	chr6:11112400-11112600	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr6:11112400-11112600	Weak transcription	Fetal Intestine Large	intestine
50	chr6:11112400-11112600	Enhancers	Monocytes-CD14+_RO01746	blood

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