Variant report

Variant	rs6799109
Chromosome Location	chr3:120458173-120458174
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	CEBPB	chr3:120458107-120458254	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:120457859..120461231-chr3:120462100..120464512,3	K562	blood:
2	chr3:120456023..120459127-chr3:120459888..120461949,3	MCF-7	breast:
3	chr3:120457859..120460564-chr3:120461782..120464733,3	K562	blood:
4	chr3:120456048..120458212-chr3:120459469..120461688,2	MCF-7	breast:

Variant related genes	Relation type
GTF2E1	TF binding region
ENSG00000153767	Chromatin interaction
ENSG00000144840	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs16831597	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16831660	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16831695	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs55866013	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv829699	chr3:120308332-120484695	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
4	nsv869548	chr3:120320731-121076337	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv916869	chr3:120360281-120973169	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv877378	chr3:120381530-120606438	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120416400-120460600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr3:120416800-120460600	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr3:120423000-120460200	Weak transcription	HUVEC	blood vessel
4	chr3:120438400-120460200	Weak transcription	NHEK	skin
5	chr3:120438400-120460600	Weak transcription	Brain Anterior Caudate	brain
6	chr3:120438400-120460600	Weak transcription	Right Ventricle	heart
7	chr3:120438600-120460000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr3:120438600-120460400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr3:120439000-120460200	Weak transcription	Primary B cells from cord blood	blood
10	chr3:120439200-120460200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:120439800-120460200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr3:120441400-120460000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr3:120442600-120460400	Weak transcription	Brain Substantia Nigra	brain
14	chr3:120443800-120460200	Weak transcription	HSMM	muscle
15	chr3:120445000-120460600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:120446800-120460400	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr3:120447200-120460200	Weak transcription	Brain Angular Gyrus	brain
18	chr3:120447200-120460600	Weak transcription	Fetal Heart	heart
19	chr3:120447600-120460200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:120447600-120460200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr3:120448200-120460200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr3:120448200-120460200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr3:120448200-120460200	Weak transcription	Primary B cells from peripheral blood	blood
24	chr3:120448200-120460200	Weak transcription	Colon Smooth Muscle	Colon
25	chr3:120448400-120460200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:120449800-120460200	Weak transcription	Adipose Nuclei	Adipose
27	chr3:120450600-120460200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr3:120455000-120459600	Weak transcription	Dnd41	blood
29	chr3:120455000-120460400	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr3:120455200-120460600	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr3:120455800-120458200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr3:120456400-120458800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
33	chr3:120456800-120458800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
34	chr3:120456800-120460000	Weak transcription	Primary T cells from cord blood	blood
35	chr3:120456800-120460200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr3:120456800-120460200	Weak transcription	HMEC	breast
37	chr3:120456800-120460600	Weak transcription	Brain Hippocampus Middle	brain
38	chr3:120457000-120460200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr3:120457200-120460000	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr3:120457400-120458400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:120457400-120460000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr3:120457400-120460200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:120457400-120460200	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr3:120457400-120460200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr3:120457400-120460200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr3:120457400-120460200	Weak transcription	Liver	Liver
47	chr3:120457400-120460200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr3:120457400-120460200	Weak transcription	Fetal Intestine Large	intestine
49	chr3:120457400-120460200	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr3:120457400-120460200	Weak transcription	Rectal Mucosa Donor 31	rectum

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