Variant report

Variant	rs3738182
Chromosome Location	chr1:221057662-221057663
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	SUZ12	chr1:221056966-221063617	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr1:221057535-221058221	H1-neurons	neurons:	n/a	n/a
3	POLR2A	chr1:221057572-221058274	H1-neurons	neurons:	n/a	n/a
4	GABPA	chr1:221057655-221058158	H1-hESC	embryonic stem cell:	n/a	n/a
5	SUZ12	chr1:221057110-221059071	NT2-D1	testis:	n/a	n/a
6	CTBP2	chr1:221057409-221059013	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:221052350..221054079-chr1:221057188..221058712,2	K562	blood:

Variant related genes	Relation type
HLA-AS1	TF binding region
ENSG00000257551	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs2184658	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2247213	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2738752	1.00[ASN][1000 genomes]
rs2738755	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34180575	0.99[EUR][1000 genomes]
rs3806325	0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs58040980	0.83[AFR][1000 genomes]
rs6682092	0.85[AFR][1000 genomes]
rs949994	0.86[LWK][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes]

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	nsv997685	chr1:220993527-221863416	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv535299	chr1:220993527-221863416	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
3	esv1798350	chr1:221020278-221069740	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3738182	RP11-295M18.2	cis	lung	GTEx

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:221052000-221058000	Active TSS	Duodenum Smooth Muscle	Duodenum
2	chr1:221054800-221058400	Weak transcription	K562	blood
3	chr1:221054800-221061000	Weak transcription	HSMM	muscle
4	chr1:221055000-221058800	Weak transcription	Ovary	ovary
5	chr1:221055800-221057800	Strong transcription	Spleen	Spleen
6	chr1:221055800-221058000	Weak transcription	Psoas Muscle	Psoas
7	chr1:221055800-221060400	Weak transcription	Hela-S3	cervix
8	chr1:221056000-221057800	Genic enhancers	Liver	Liver
9	chr1:221056000-221058000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:221056000-221058000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
11	chr1:221056000-221061000	Weak transcription	NHDF-Ad	bronchial
12	chr1:221056200-221058000	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
13	chr1:221056200-221058600	Bivalent Enhancer	Fetal Stomach	stomach
14	chr1:221056200-221059200	Strong transcription	Osteobl	bone
15	chr1:221056200-221060400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr1:221056400-221059000	Strong transcription	Muscle Satellite Cultured Cells	--
17	chr1:221056400-221060200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:221056600-221057800	Bivalent/Poised TSS	Fetal Intestine Small	intestine
19	chr1:221056600-221058400	Genic enhancers	Fetal Muscle Trunk	muscle
20	chr1:221056600-221060000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:221056600-221060400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:221056800-221057800	Genic enhancers	Primary monocytes fromperipheralblood	blood
23	chr1:221056800-221057800	Transcr. at gene 5' and 3'	Fetal Adrenal Gland	Adrenal Gland
24	chr1:221056800-221058600	Weak transcription	Primary B cells from cord blood	blood
25	chr1:221056800-221059200	Transcr. at gene 5' and 3'	Colon Smooth Muscle	Colon
26	chr1:221056800-221059400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:221056800-221060400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:221057000-221058400	Bivalent Enhancer	Fetal Heart	heart
29	chr1:221057000-221060000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:221057000-221060200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:221057000-221060400	Genic enhancers	Primary neutrophils fromperipheralblood	blood
32	chr1:221057000-221061800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
33	chr1:221057200-221057800	Flanking Bivalent TSS/Enh	Fetal Lung	lung
34	chr1:221057200-221057800	Flanking Active TSS	Rectal Smooth Muscle	rectum
35	chr1:221057200-221058000	ZNF genes & repeats	Esophagus	oesophagus
36	chr1:221057200-221058200	Transcr. at gene 5' and 3'	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr1:221057200-221058200	Genic enhancers	Left Ventricle	heart
38	chr1:221057200-221058400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr1:221057200-221058600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr1:221057200-221059000	Genic enhancers	Placenta	Placenta
41	chr1:221057200-221059000	Genic enhancers	Lung	lung
42	chr1:221057200-221059400	Strong transcription	HUVEC	blood vessel
43	chr1:221057200-221059800	Strong transcription	Skeletal Muscle Male	skeletal muscle
44	chr1:221057200-221060000	Strong transcription	NHLF	lung
45	chr1:221057400-221057800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
46	chr1:221057400-221057800	Enhancers	Right Atrium	heart
47	chr1:221057400-221058000	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:221057400-221058000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
49	chr1:221057400-221058000	Bivalent/Poised TSS	Fetal Intestine Large	intestine
50	chr1:221057400-221058000	Genic enhancers	Right Ventricle	heart

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