Variant report

Variant	rs6799691
Chromosome Location	chr3:119196781-119196782
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	POLR2A	chr3:119196667-119196855	K562	blood:	n/a	n/a
2	TAL1	chr3:119196610-119196906	K562	blood:	n/a	chr3:119196756-119196774

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:119185648..119192167-chr3:119194088..119200916,11	MCF-7	breast:

Variant related genes	Relation type
POGLUT1	TF binding region
ENSG00000163389	Chromatin interaction
ENSG00000176142	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs3732419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687860	0.90[AFR][1000 genomes]
rs610902	0.82[ASN][1000 genomes]
rs6414282	0.87[AFR][1000 genomes]
rs6438532	0.95[YRI][hapmap]
rs6777535	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs6794833	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7430798	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs9289129	0.86[YRI][hapmap]

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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv829695	chr3:119178890-119367996	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6799691	POGLUT1	cis	Artery Tibial	GTEx
rs6799691	KTELC1	cis	multi-tissue	Pritchard
rs6799691	KTELC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119188400-119216200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:119188400-119216800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:119188600-119198000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:119188600-119216200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:119188800-119216200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:119189000-119196800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr3:119189000-119197000	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr3:119189000-119198000	Weak transcription	HSMM	muscle
9	chr3:119189000-119198200	Weak transcription	NH-A	brain
10	chr3:119189000-119199200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr3:119189000-119204400	Weak transcription	NHDF-Ad	bronchial
12	chr3:119189000-119216200	Weak transcription	Stomach Mucosa	stomach
13	chr3:119189000-119216200	Weak transcription	HUVEC	blood vessel
14	chr3:119189000-119216600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:119189200-119199000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:119189200-119199600	Weak transcription	HMEC	breast
17	chr3:119189200-119203000	Weak transcription	Fetal Kidney	kidney
18	chr3:119189400-119201800	Strong transcription	Fetal Stomach	stomach
19	chr3:119189600-119205400	Weak transcription	Hela-S3	cervix
20	chr3:119189600-119209200	Strong transcription	Primary B cells from cord blood	blood
21	chr3:119189600-119211800	Strong transcription	Primary B cells from peripheral blood	blood
22	chr3:119189600-119211800	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr3:119189800-119198800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:119189800-119199000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr3:119189800-119200800	Strong transcription	Fetal Thymus	thymus
26	chr3:119189800-119210000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr3:119189800-119211400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
28	chr3:119189800-119212200	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr3:119189800-119216000	Weak transcription	Fetal Heart	heart
30	chr3:119190000-119201200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr3:119190000-119201800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:119190000-119202000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr3:119190000-119211800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr3:119190000-119212200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr3:119190000-119212200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr3:119190200-119200200	Strong transcription	Primary T helper naive cells from peripheral blood	blood
37	chr3:119190400-119199200	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr3:119190400-119212200	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr3:119190600-119199200	Strong transcription	Duodenum Mucosa	Duodenum
40	chr3:119190600-119204800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr3:119190600-119211800	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr3:119190600-119212000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr3:119190800-119199800	Weak transcription	Fetal Lung	lung
44	chr3:119190800-119204200	Weak transcription	A549	lung
45	chr3:119190800-119204200	Weak transcription	HSMMtube	muscle
46	chr3:119190800-119205000	Weak transcription	Psoas Muscle	Psoas
47	chr3:119190800-119216400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr3:119191000-119198000	Weak transcription	NHEK	skin
49	chr3:119191000-119203200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr3:119191000-119216400	Weak transcription	Fetal Brain Male	brain

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