Variant report

Variant	rs9350832
Chromosome Location	chr6:80578416-80578417
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	CTCF	chr6:80578360-80578510	HUVEC	blood vessel:	n/a	n/a
2	CTCF	chr6:80577612-80578480	A549	lung:	n/a	chr6:80578027-80578040 chr6:80578020-80578041 chr6:80578026-80578042 chr6:80578025-80578043
3	MAX	chr6:80577920-80578521	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr6:80578320-80578470	GM12872	blood:	n/a	n/a
5	SMC3	chr6:80577360-80578430	SK-N-SH	brain:	n/a	chr6:80578027-80578041 chr6:80578027-80578037
6	RAD21	chr6:80577105-80580479	SK-N-SH	brain:	n/a	chr6:80578023-80578042 chr6:80579004-80579018 chr6:80579461-80579475 chr6:80579484-80579498 chr6:80578027-80578037 chr6:80579477-80579496
7	CTCF	chr6:80578280-80578430	GM12864	blood:	n/a	n/a
8	CTCF	chr6:80578360-80578510	AG04450	lung:	n/a	n/a
9	GATA2	chr6:80577519-80578558	SH-SY5Y	brain:	n/a	n/a
10	CTCF	chr6:80578360-80578510	HFF	foreskin:	n/a	n/a
11	CTCF	chr6:80578320-80578570	GM12873	blood:	n/a	n/a
12	CTCF	chr6:80578320-80578470	HMF	breast:	n/a	n/a
13	CTCF	chr6:80577346-80578651	SK-N-SH	brain:	n/a	chr6:80578027-80578040 chr6:80578020-80578041 chr6:80578026-80578042 chr6:80578025-80578043

No.	Distal block	Cell Line	Cell type
1	chr6:80423120..80423711-chr6:80577789..80578553,2	K562	blood:
2	chr6:80577908..80579667-chr6:80713971..80715630,2	K562	blood:
3	chr6:80487430..80488393-chr6:80577490..80578546,7	K562	blood:
4	chr6:80577959..80580872-chr6:80588146..80590140,2	K562	blood:
5	chr6:80571013..80573087-chr6:80576802..80579710,2	K562	blood:

Variant related genes	Relation type
ENSG00000233835	TF binding region
ENSG00000112742	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs34285052	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71565054	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9341798	0.83[ASN][1000 genomes]
rs9343943	0.88[CEU][hapmap];0.82[JPT][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9343946	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9352776	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9352779	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9448843	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs992015	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028607	chr6:79853272-80767716	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1032347	chr6:80284809-80694778	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1021143	chr6:80400195-80598163	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	esv3693359	chr6:80539454-80606537	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:80576600-80582200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:80577400-80583400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:80577600-80579400	Enhancers	Dnd41	blood
4	chr6:80577600-80579800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:80577600-80580000	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr6:80577600-80583200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr6:80577800-80578600	Enhancers	H1 Cell Line	embryonic stem cell
8	chr6:80577800-80578600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr6:80577800-80578600	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr6:80577800-80578600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:80577800-80578600	Enhancers	Fetal Thymus	thymus
12	chr6:80577800-80579400	Enhancers	Ovary	ovary
13	chr6:80577800-80580000	Enhancers	Fetal Heart	heart
14	chr6:80577800-80580200	Enhancers	HMEC	breast
15	chr6:80578000-80578600	Enhancers	Primary T cells fromperipheralblood	blood
16	chr6:80578000-80579000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr6:80578000-80579000	Weak transcription	Fetal Stomach	stomach
18	chr6:80578000-80579200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr6:80578000-80579200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr6:80578000-80579200	Weak transcription	Brain Hippocampus Middle	brain
21	chr6:80578000-80579200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr6:80578000-80579200	Weak transcription	Fetal Intestine Small	intestine
23	chr6:80578000-80579200	Weak transcription	Placenta	Placenta
24	chr6:80578000-80579200	Weak transcription	NHDF-Ad	bronchial
25	chr6:80578000-80579400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr6:80578000-80579400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr6:80578000-80579400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr6:80578000-80579400	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr6:80578000-80579400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr6:80578000-80579400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr6:80578000-80579400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr6:80578000-80579400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr6:80578000-80579400	Weak transcription	Fetal Brain Female	brain
34	chr6:80578000-80579400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr6:80578000-80579400	Weak transcription	A549	lung
36	chr6:80578000-80579400	Weak transcription	Osteobl	bone
37	chr6:80578000-80579600	Enhancers	Liver	Liver
38	chr6:80578000-80579600	Weak transcription	Colon Smooth Muscle	Colon
39	chr6:80578000-80580000	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr6:80578000-80582800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr6:80578200-80578600	Enhancers	Pancreas	Pancrea
42	chr6:80578200-80579200	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr6:80578200-80579200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr6:80578200-80579200	Weak transcription	Hela-S3	cervix
45	chr6:80578200-80579400	Weak transcription	Adipose Nuclei	Adipose
46	chr6:80578200-80579400	Weak transcription	Brain Cingulate Gyrus	brain
47	chr6:80578200-80579400	Weak transcription	Brain Substantia Nigra	brain
48	chr6:80578200-80579600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr6:80578400-80578600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
50	chr6:80578400-80578600	Enhancers	Rectal Mucosa Donor 31	rectum

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