Variant report

Variant	rs12401738
Chromosome Location	chr1:78446761-78446762
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	chr1:78443332-78446830	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:78441900..78447727-chr1:78466477..78473207,15	MCF-7	breast:
2	chr1:78441980..78446801-chr1:78467462..78471771,12	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DNAJB4-1	chr1:78444779-78456066	NONHSAT004062

Variant related genes	Relation type
FUBP1	TF binding region
ENSG00000273338	Chromatin interaction
ENSG00000162616	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12409958	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.93[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];0.83[TSI][hapmap];0.87[YRI][hapmap]
rs12411130	0.87[ASW][hapmap];0.89[CEU][hapmap];0.96[GIH][hapmap];0.93[LWK][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12742653	1.00[CEU][hapmap]
rs4130548	1.00[CEU][hapmap];0.96[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9729667	1.00[CEU][hapmap];0.96[GIH][hapmap];0.91[MEX][hapmap];0.86[TSI][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	esv1794082	chr1:78102426-78492221	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
2	esv3434340	chr1:78153780-78607103	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv518855	chr1:78416669-78456355	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12401738	IFI44	cis	parietal	SCAN
rs12401738	TYW3	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:78441400-78446800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr1:78442000-78446800	Active TSS	GM12878-XiMat	blood
3	chr1:78442000-78447200	Active TSS	A549	lung
4	chr1:78442600-78447000	Active TSS	Right Ventricle	heart
5	chr1:78442800-78446800	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr1:78442800-78447200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr1:78442800-78447200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:78443000-78446800	Active TSS	HMEC	breast
9	chr1:78443000-78447000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:78443000-78447600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr1:78443600-78446800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:78443600-78447000	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr1:78445800-78449600	Weak transcription	Stomach Mucosa	stomach
14	chr1:78445800-78449800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr1:78446000-78446800	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr1:78446000-78446800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
17	chr1:78446000-78446800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:78446000-78446800	Enhancers	Colon Smooth Muscle	Colon
19	chr1:78446000-78446800	Weak transcription	Left Ventricle	heart
20	chr1:78446000-78446800	Weak transcription	Lung	lung
21	chr1:78446000-78447000	Weak transcription	Ovary	ovary
22	chr1:78446000-78447000	Weak transcription	Pancreas	Pancrea
23	chr1:78446000-78447200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr1:78446000-78447200	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr1:78446000-78447200	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr1:78446000-78447200	Enhancers	Liver	Liver
27	chr1:78446000-78447400	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr1:78446000-78448200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:78446000-78448200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:78446000-78449800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr1:78446000-78449800	Weak transcription	Small Intestine	intestine
32	chr1:78446000-78451800	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr1:78446000-78452600	Weak transcription	Gastric	stomach
34	chr1:78446000-78455600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr1:78446000-78458600	Weak transcription	Fetal Muscle Trunk	muscle
36	chr1:78446000-78458800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr1:78446000-78461000	Weak transcription	Placenta	Placenta
38	chr1:78446200-78446800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr1:78446200-78446800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
40	chr1:78446200-78446800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
41	chr1:78446200-78446800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr1:78446200-78446800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
43	chr1:78446200-78446800	Enhancers	Brain Substantia Nigra	brain
44	chr1:78446200-78446800	Flanking Active TSS	Hela-S3	cervix
45	chr1:78446200-78446800	Flanking Active TSS	Osteobl	bone
46	chr1:78446200-78447000	Transcr. at gene 5' and 3'	HSMM	muscle
47	chr1:78446200-78447000	Flanking Active TSS	HUVEC	blood vessel
48	chr1:78446200-78447800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
49	chr1:78446200-78448400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr1:78446200-78449400	Weak transcription	Fetal Intestine Large	intestine

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