Variant report

Variant	rs6794707
Chromosome Location	chr3:105230122-105230123
allele	A/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	STAT3	chr3:105230072-105230272	MCF10A-Er-Src	breast:	n/a	n/a
2	GATA3	chr3:105229988-105230175	SH-SY5Y	brain:	n/a	chr3:105230145-105230162
3	GATA3	chr3:105229755-105230468	SK-N-SH	brain:	n/a	chr3:105230311-105230318 chr3:105230145-105230162
4	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: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11720296	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3957514	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6769557	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6776188	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6776462	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6792010	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7613684	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs901278	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9288809	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9851104	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9873500	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	chr3:105222800-105230400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr3:105222800-105231800	Weak transcription	NH-A	brain
7	chr3:105222800-105246000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr3:105223800-105274800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:105224400-105239600	Weak transcription	GM12878-XiMat	blood
10	chr3:105225800-105236000	Weak transcription	Liver	Liver
11	chr3:105226800-105230200	Weak transcription	Brain Cingulate Gyrus	brain
12	chr3:105227000-105231600	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr3:105227000-105232000	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr3:105227400-105233800	Weak transcription	Brain Substantia Nigra	brain
15	chr3:105228400-105230600	Weak transcription	Brain Hippocampus Middle	brain
16	chr3:105228800-105230800	Enhancers	Brain Angular Gyrus	brain
17	chr3:105228800-105233200	Enhancers	Osteobl	bone
18	chr3:105229000-105230200	Enhancers	H9 Cell Line	embryonic stem cell
19	chr3:105229000-105230200	Enhancers	Gastric	stomach
20	chr3:105229000-105230600	Enhancers	HSMM	muscle
21	chr3:105229400-105233200	Enhancers	NHDF-Ad	bronchial
22	chr3:105229600-105231800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr3:105229600-105232800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr3:105229600-105244600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:105229600-105260400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr3:105229800-105230400	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr3:105229800-105233000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:105229800-105233200	Enhancers	Muscle Satellite Cultured Cells	--
29	chr3:105229800-105235000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:105230000-105230600	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr3:105230000-105230600	Enhancers	A549	lung
32	chr3:105230000-105231400	Enhancers	Brain Anterior Caudate	brain
33	chr3:105230000-105233400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr3:105230000-105234200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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