Variant report

Variant	rs3748140
Chromosome Location	chr8:8999019-8999020
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	chr8:8997466-8999259	K562	blood:	n/a	n/a
2	POLR2A	chr8:8998832-8999194	A549	lung:	n/a	n/a
3	POLR2A	chr8:8991597-8999830	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr8:8998952-8999050	GM12878	blood:	n/a	n/a
5	POLR2A	chr8:8998947-8999130	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr8:8998729-8999356	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr8:8998858-9000821	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000254340	TF binding region

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10087078	1.00[JPT][hapmap]
rs17155163	1.00[CEU][hapmap]
rs2898209	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55642015	0.92[EUR][1000 genomes]
rs6982039	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6998837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6999855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7011581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7013211	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73512435	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7819910	0.82[EUR][1000 genomes]
rs7838663	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917117	chr8:8621658-9313799	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1022468	chr8:8857853-9209167	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv539460	chr8:8857853-9209167	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv817373	chr8:8857854-9361049	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv1022328	chr8:8954003-9061281	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv610206	chr8:8961017-9162048	Genic enhancers Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv1026279	chr8:8982622-9030279	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	n/a
8	nsv949434	chr8:8993551-9318404	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Alzheimer's disease	22832961	GWAS catalog

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:8992600-9000000	Weak transcription	Hela-S3	cervix
2	chr8:8993600-9005400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr8:8993800-9007400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr8:8994200-9000800	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr8:8994200-9005600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr8:8994200-9007200	Weak transcription	Brain Angular Gyrus	brain
7	chr8:8994200-9007200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr8:8994200-9007200	Weak transcription	Fetal Brain Male	brain
9	chr8:8994400-9001000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr8:8994400-9005200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr8:8994400-9005200	Weak transcription	Small Intestine	intestine
12	chr8:8994600-8999600	Genic enhancers	HUVEC	blood vessel
13	chr8:8994600-9000400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr8:8994800-8999800	Strong transcription	Fetal Stomach	stomach
15	chr8:8994800-8999800	Strong transcription	Stomach Smooth Muscle	stomach
16	chr8:8994800-9000000	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr8:8994800-9000600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr8:8994800-9001000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr8:8994800-9001000	Strong transcription	Fetal Muscle Trunk	muscle
20	chr8:8994800-9001800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr8:8995000-8999200	Strong transcription	NHDF-Ad	bronchial
22	chr8:8995000-8999400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
23	chr8:8995000-9000600	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr8:8995000-9000800	Strong transcription	H1 Cell Line	embryonic stem cell
25	chr8:8995200-8999200	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr8:8995200-8999800	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr8:8995200-9000800	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr8:8995200-9000800	Strong transcription	Fetal Muscle Leg	muscle
29	chr8:8995200-9004800	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr8:8995400-8999400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr8:8995400-9000600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr8:8995400-9001000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr8:8995600-9000600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr8:8996200-8999200	Strong transcription	Muscle Satellite Cultured Cells	--
35	chr8:8996200-8999600	Strong transcription	Aorta	Aorta
36	chr8:8996200-8999600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr8:8996200-8999800	Strong transcription	Primary T cells from cord blood	blood
38	chr8:8996200-9000400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
39	chr8:8996200-9000800	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr8:8996200-9001800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr8:8996400-8999400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
42	chr8:8996400-8999800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr8:8996400-9000800	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr8:8996600-8999200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr8:8996600-8999200	Strong transcription	Placenta Amnion	Placenta Amnion
46	chr8:8996600-9000400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr8:8996600-9000600	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr8:8996800-8999200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr8:8996800-8999200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
50	chr8:8996800-8999200	Strong transcription	NHLF	lung

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