Variant report

Variant	rs6770045
Chromosome Location	chr3:105229911-105229912
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	GATA3	chr3:105229755-105230468	SK-N-SH	brain:	n/a	chr3:105230311-105230318 chr3:105230145-105230162
2	GATA3	chr3:105229752-105230497	SK-N-SH	brain:	n/a	chr3:105230311-105230318 chr3:105230145-105230162

Variant related genes	Relation type
ALCAM	TF binding region

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

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

rs_ID	r²[population]
rs2171147	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3772558	0.88[AFR][1000 genomes]
rs3821492	0.86[AFR][1000 genomes]
rs73854324	0.80[AFR][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	nsv525071	chr3:105004853-105409321	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv829650	chr3:105070893-105255036	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv534224	chr3:105141696-105404293	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv829651	chr3:105203424-105402136	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv460811	chr3:105212993-105316769	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv591240	chr3:105212993-105316769	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105210200-105243200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:105221400-105300400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:105221600-105231800	Weak transcription	NHLF	lung
4	chr3:105222200-105260600	Weak transcription	Fetal Kidney	kidney
5	chr3:105222600-105230000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr3:105222800-105230400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr3:105222800-105231800	Weak transcription	NH-A	brain
8	chr3:105222800-105246000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:105223000-105230000	Weak transcription	A549	lung
10	chr3:105223800-105274800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:105224400-105239600	Weak transcription	GM12878-XiMat	blood
12	chr3:105225800-105236000	Weak transcription	Liver	Liver
13	chr3:105226800-105230200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr3:105227000-105230000	Weak transcription	Brain Anterior Caudate	brain
15	chr3:105227000-105231600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr3:105227000-105232000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr3:105227400-105233800	Weak transcription	Brain Substantia Nigra	brain
18	chr3:105228400-105230600	Weak transcription	Brain Hippocampus Middle	brain
19	chr3:105228800-105230800	Enhancers	Brain Angular Gyrus	brain
20	chr3:105228800-105233200	Enhancers	Osteobl	bone
21	chr3:105229000-105230200	Enhancers	H9 Cell Line	embryonic stem cell
22	chr3:105229000-105230200	Enhancers	Gastric	stomach
23	chr3:105229000-105230600	Enhancers	HSMM	muscle
24	chr3:105229400-105230000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr3:105229400-105233200	Enhancers	NHDF-Ad	bronchial
26	chr3:105229600-105231800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:105229600-105232800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr3:105229600-105244600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr3:105229600-105260400	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr3:105229800-105230000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr3:105229800-105230400	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr3:105229800-105233000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr3:105229800-105233200	Enhancers	Muscle Satellite Cultured Cells	--
34	chr3:105229800-105235000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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