Variant report

Variant	rs13323843
Chromosome Location	chr3:105231921-105231922
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	MAX	chr3:105231881-105232232	SK-N-SH	brain:	n/a	chr3:105232163-105232172
2	NFIC	chr3:105231802-105232381	SK-N-SH	brain:	n/a	chr3:105232151-105232168 chr3:105232026-105232043
3	JUND	chr3:105231699-105232292	SK-N-SH	brain:	n/a	n/a
4	FOSL2	chr3:105231769-105232384	SK-N-SH	brain:	n/a	n/a
5	TCF12	chr3:105231716-105232485	SK-N-SH	brain:	n/a	n/a
6	TEAD4	chr3:105231857-105232437	SK-N-SH	brain:	n/a	n/a
7	MEF2A	chr3:105231888-105232280	SK-N-SH	brain:	n/a	chr3:105231960-105231975
8	GATA3	chr3:105231671-105233274	SK-N-SH	brain:	n/a	n/a
9	TCF12	chr3:105231678-105232462	SK-N-SH	brain:	n/a	n/a
10	PBX3	chr3:105231888-105232267	SK-N-SH	brain:	n/a	n/a
11	FOSL2	chr3:105231843-105232233	SK-N-SH	brain:	n/a	n/a
12	EP300	chr3:105231673-105232370	SK-N-SH	brain:	n/a	n/a
13	EP300	chr3:105231879-105232171	SK-N-SH_RA	brain:	n/a	n/a
14	NFIC	chr3:105231738-105232526	SK-N-SH	brain:	n/a	chr3:105232151-105232168 chr3:105232026-105232043
15	TEAD4	chr3:105231777-105232464	SK-N-SH	brain:	n/a	n/a
16	GATA3	chr3:105231637-105232502	SK-N-SH	brain:	n/a	n/a
17	JUND	chr3:105231768-105232401	SK-N-SH	brain:	n/a	n/a
18	JUND	chr3:105231703-105232440	SK-N-SH	brain:	n/a	n/a
19	EP300	chr3:105231751-105232407	SK-N-SH	brain:	n/a	n/a
20	RXRA	chr3:105231772-105232250	SK-N-SH	brain:	n/a	n/a
21	PBX3	chr3:105231771-105232430	SK-N-SH	brain:	n/a	n/a
22	POLR2A	chr3:105231853-105232276	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
ALCAM	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11559013	0.86[AFR][1000 genomes]
rs13317567	0.86[AFR][1000 genomes]
rs16851209	0.98[EUR][1000 genomes]
rs2033803	0.88[EUR][1000 genomes]
rs3772558	0.97[ASN][1000 genomes]
rs59857604	0.81[EUR][1000 genomes]
rs73854323	0.91[AFR][1000 genomes]
rs7651616	0.81[EUR][1000 genomes]
rs7651901	0.81[EUR][1000 genomes]
rs9815659	0.81[EUR][1000 genomes]
rs9846962	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9848760	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9875739	0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[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:42 , 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	chr3:105222200-105260600	Weak transcription	Fetal Kidney	kidney
4	chr3:105222800-105246000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:105223800-105274800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:105224400-105239600	Weak transcription	GM12878-XiMat	blood
7	chr3:105225800-105236000	Weak transcription	Liver	Liver
8	chr3:105227000-105232000	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr3:105227400-105233800	Weak transcription	Brain Substantia Nigra	brain
10	chr3:105228800-105233200	Enhancers	Osteobl	bone
11	chr3:105229400-105233200	Enhancers	NHDF-Ad	bronchial
12	chr3:105229600-105232800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:105229600-105244600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:105229600-105260400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr3:105229800-105233000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr3:105229800-105233200	Enhancers	Muscle Satellite Cultured Cells	--
17	chr3:105229800-105235000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:105230000-105233400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:105230000-105234200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr3:105230200-105232600	Enhancers	Brain Cingulate Gyrus	brain
21	chr3:105230200-105262600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr3:105230400-105232400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:105230400-105234200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr3:105230600-105232000	Weak transcription	HSMMtube	muscle
25	chr3:105230600-105232400	Enhancers	Fetal Heart	heart
26	chr3:105230600-105233800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr3:105230800-105234200	Weak transcription	Brain Angular Gyrus	brain
28	chr3:105231000-105237400	Weak transcription	Pancreatic Islets	Pancreatic Islet
29	chr3:105231200-105232000	Weak transcription	Brain Hippocampus Middle	brain
30	chr3:105231400-105232200	Weak transcription	Brain Anterior Caudate	brain
31	chr3:105231400-105234200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:105231600-105232200	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr3:105231600-105233400	Enhancers	HSMM	muscle
34	chr3:105231800-105232200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr3:105231800-105232200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:105231800-105232200	Enhancers	A549	lung
37	chr3:105231800-105232200	Enhancers	NHEK	skin
38	chr3:105231800-105232600	Enhancers	NHLF	lung
39	chr3:105231800-105232800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr3:105231800-105232800	Enhancers	NH-A	brain
41	chr3:105231800-105233200	Enhancers	HMEC	breast
42	chr3:105231800-105234600	Enhancers	ES-I3 Cell Line	embryonic stem cell

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