Variant report

Variant	rs3748017
Chromosome Location	chr1:95006158-95006159
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	POLR2A	chr1:95005611-95008251	Hela-S3	cervix:	n/a	n/a
2	GTF2F1	chr1:95006125-95006907	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr1:95006048-95007983	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr1:94991604-95010849	IMR90	lung:	n/a	n/a
5	POLR2A	chr1:95006117-95008373	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr1:95000323-95009541	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr1:95003836-95008278	U87	brain:	n/a	n/a
8	CHD1	chr1:94994939-95011321	IMR90	lung:	n/a	n/a
9	MAFK	chr1:95005921-95006963	Hela-S3	cervix:	n/a	chr1:95006888-95006903 chr1:95006721-95006738
10	USF2	chr1:95005863-95006897	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr1:95004799-95008370	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr1:95006041-95007962	U87	brain:	n/a	n/a
13	POLR2A	chr1:95004630-95008333	MCF10A-Er-Src	breast:	n/a	n/a
14	POLR2A	chr1:95006088-95008209	Hela-S3	cervix:	n/a	n/a
15	TCF7L2	chr1:95006129-95006571	Hela-S3	cervix:	n/a	n/a
16	MAX	chr1:95005063-95008387	Hela-S3	cervix:	n/a	chr1:95006717-95006724 chr1:95006812-95006821
17	RFX5	chr1:95005068-95007782	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr1:94999692-95008368	ProgFib	skin:	n/a	n/a
19	RAD21	chr1:95006121-95006785	Hela-S3	cervix:	n/a	n/a
20	TBP	chr1:95005043-95006937	Hela-S3	cervix:	n/a	n/a
21	MAZ	chr1:95004703-95008397	IMR90	lung:	n/a	chr1:95006717-95006724 chr1:95006812-95006821

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:95004121..95007110-chr1:95017554..95021316,3	MCF-7	breast:

Variant related genes	Relation type
F3	TF binding region

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs2021962	0.93[AMR][1000 genomes]
rs2021963	1.00[JPT][hapmap];0.93[AMR][1000 genomes]
rs3917606	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6692345	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes]
rs698943	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs698944	1.00[JPT][hapmap]
rs725299	1.00[JPT][hapmap];0.93[AMR][1000 genomes]
rs7531358	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs841698	1.00[JPT][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	nsv531881	chr1:94937444-95053785	Weak transcription Bivalent Enhancer Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv870696	chr1:95005220-95081587	Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv871391	chr1:95005220-95083836	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94965600-95006400	Weak transcription	Colon Smooth Muscle	Colon
2	chr1:94986000-95006200	Weak transcription	Liver	Liver
3	chr1:94994600-95006200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:94995200-95006200	Weak transcription	Spleen	Spleen
5	chr1:95001200-95006400	Weak transcription	Small Intestine	intestine
6	chr1:95001400-95006600	Transcr. at gene 5' and 3'	HMEC	breast
7	chr1:95001600-95006200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr1:95001600-95007400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:95001600-95007800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:95001800-95006200	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr1:95001800-95007000	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:95001800-95007800	Active TSS	Brain Hippocampus Middle	brain
13	chr1:95002000-95006200	Weak transcription	Aorta	Aorta
14	chr1:95002400-95006600	Transcr. at gene 5' and 3'	NHLF	lung
15	chr1:95002600-95006600	Active TSS	Fetal Brain Female	brain
16	chr1:95002800-95006800	Transcr. at gene 5' and 3'	NHEK	skin
17	chr1:95002800-95007200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:95002800-95007600	Active TSS	Brain Anterior Caudate	brain
19	chr1:95003000-95007800	Active TSS	Right Atrium	heart
20	chr1:95003000-95008400	Active TSS	Brain Angular Gyrus	brain
21	chr1:95003200-95006400	Active TSS	Duodenum Smooth Muscle	Duodenum
22	chr1:95003200-95007800	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr1:95003200-95007800	Active TSS	Fetal Intestine Large	intestine
24	chr1:95003800-95007600	Active TSS	Stomach Smooth Muscle	stomach
25	chr1:95003800-95007800	Active TSS	Brain Cingulate Gyrus	brain
26	chr1:95004000-95006800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:95004200-95006200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr1:95004200-95006800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
29	chr1:95004200-95008800	Active TSS	Ovary	ovary
30	chr1:95004400-95006200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr1:95004400-95006200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr1:95004400-95006200	Active TSS	Osteobl	bone
33	chr1:95004400-95006400	Active TSS	Brain Germinal Matrix	brain
34	chr1:95004400-95006400	Active TSS	Placenta	Placenta
35	chr1:95004400-95007800	Active TSS	Left Ventricle	heart
36	chr1:95004400-95007800	Active TSS	Right Ventricle	heart
37	chr1:95004400-95007800	Active TSS	NH-A	brain
38	chr1:95004400-95008200	Active TSS	Pancreas	Pancrea
39	chr1:95004600-95006400	Active TSS	ES-I3 Cell Line	embryonic stem cell
40	chr1:95004600-95006400	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr1:95004600-95007800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:95004800-95006800	Bivalent/Poised TSS	Thymus	Thymus
43	chr1:95004800-95007800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr1:95004800-95007800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:95005000-95006200	Active TSS	Fetal Stomach	stomach
46	chr1:95005000-95006200	Enhancers	Dnd41	blood
47	chr1:95005000-95006400	Active TSS	Rectal Mucosa Donor 31	rectum
48	chr1:95005200-95006200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr1:95005200-95006200	Active TSS	HSMM	muscle
50	chr1:95005400-95006200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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