Variant report

Variant	rs3768234
Chromosome Location	chr1:85740812-85740813
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	SPI1	chr1:85740410-85741082	GM12878	blood:	n/a	n/a
2	SPI1	chr1:85740544-85740842	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:85740468-85743570	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr1:85740591-85742964	GM12891	blood:	n/a	n/a
5	PBX3	chr1:85740741-85741304	SK-N-SH	brain:	n/a	n/a
6	FOS	chr1:85740420-85741249	HUVEC	blood vessel:	n/a	chr1:85741049-85741057 chr1:85741200-85741212 chr1:85740666-85740675 chr1:85741051-85741060 chr1:85741052-85741061 chr1:85741050-85741061
7	KAP1	chr1:85740518-85742974	HEK293	kidney:	n/a	chr1:85741050-85741059
8	RELA	chr1:85740582-85742917	GM12878	blood:	n/a	chr1:85741485-85741494 chr1:85741485-85741494
9	RCOR1	chr1:85740633-85740832	GM12878	blood:	n/a	n/a
10	POLR2A	chr1:85740603-85742874	K562	blood:	n/a	n/a
11	CHD1	chr1:85740696-85742142	GM12878	blood:	n/a	n/a
12	HCFC1	chr1:85740700-85743065	Hela-S3	cervix:	n/a	n/a
13	FOSL2	chr1:85740694-85741323	A549	lung:	n/a	chr1:85741049-85741057 chr1:85741200-85741212 chr1:85741051-85741060 chr1:85741052-85741061
14	RELA	chr1:85740690-85742803	GM19099	blood:	n/a	chr1:85741485-85741494 chr1:85741485-85741494
15	POLR2A	chr1:85740638-85742911	GM12878	blood:	n/a	n/a
16	POLR2A	chr1:85740399-85742970	HUVEC	blood vessel:	n/a	n/a
17	JUN	chr1:85740610-85741328	HUVEC	blood vessel:	n/a	chr1:85741049-85741057 chr1:85741200-85741212 chr1:85740666-85740675 chr1:85741051-85741060 chr1:85741052-85741061
18	SPI1	chr1:85740475-85740964	GM12891	blood:	n/a	n/a
19	SPI1	chr1:85740481-85740974	HL-60	blood:	n/a	n/a
20	POLR2A	chr1:85740800-85743131	MCF10A-Er-Src	breast:	n/a	n/a
21	SPI1	chr1:85740536-85740905	GM12891	blood:	n/a	n/a
22	MAZ	chr1:85740442-85742959	IMR90	lung:	n/a	chr1:85741944-85741954
23	TBP	chr1:85740767-85740964	GM12878	blood:	n/a	n/a
24	EP300	chr1:85740591-85740814	GM12878	blood:	n/a	chr1:85740611-85740625
25	SETDB1	chr1:85740560-85741221	U2OS	brain:	n/a	n/a
26	TCF7L2	chr1:85740418-85741313	HEK293	kidney:	n/a	chr1:85741051-85741060
27	POLR2A	chr1:85740674-85742810	HUVEC	blood vessel:	n/a	n/a
28	ZNF263	chr1:85740563-85742748	HEK293-T-REx	kidney:	n/a	n/a
29	GATA2	chr1:85740398-85741192	HUVEC	blood vessel:	n/a	chr1:85740666-85740676 chr1:85740588-85740597 chr1:85741053-85741062
30	GTF2F1	chr1:85740785-85741187	Hela-S3	cervix:	n/a	n/a
31	IKZF1	chr1:85740657-85741112	GM12878	blood:	n/a	n/a
32	KAP1	chr1:85740471-85741812	U2OS	brain:	n/a	chr1:85741050-85741059
33	POLR2A	chr1:85739539-85742754	HUVEC	blood vessel:	n/a	n/a
34	POLR2A	chr1:85740607-85741150	HUVEC	blood vessel:	n/a	n/a
35	FOSL2	chr1:85740771-85741404	SK-N-SH	brain:	n/a	chr1:85741049-85741057 chr1:85741200-85741212 chr1:85741051-85741060 chr1:85741052-85741061
36	POLR2A	chr1:85738277-85742976	IMR90	lung:	n/a	n/a
37	SMARCC1	chr1:85740739-85742925	Hela-S3	cervix:	n/a	chr1:85741051-85741060
38	POLR2A	chr1:85739932-85743153	Hela-S3	cervix:	n/a	n/a
39	PBX3	chr1:85740789-85741253	SK-N-SH	brain:	n/a	n/a
40	JUND	chr1:85740713-85741331	SK-N-SH	brain:	n/a	chr1:85741050-85741061 chr1:85741049-85741057 chr1:85741200-85741212 chr1:85741051-85741060 chr1:85741052-85741061
41	POLR2A	chr1:85740321-85742971	HUVEC	blood vessel:	n/a	n/a
42	MAZ	chr1:85740790-85740896	GM12878	blood:	n/a	n/a
43	POLR2A	chr1:85740575-85743059	HUVEC	blood vessel:	n/a	n/a
44	CHD1	chr1:85739832-85743054	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:85739753..85743262-chr1:86045535..86049012,3	K562	blood:
2	chr1:85665631..85669772-chr1:85739485..85744059,5	K562	blood:
3	chr1:85740297..85741951-chr1:85930278..85931798,2	MCF-7	breast:
4	chr1:85723214..85729954-chr1:85738689..85743771,11	K562	blood:
5	chr1:85739584..85746681-chr1:86042287..86049012,10	K562	blood:

Variant related genes	Relation type
ENSG00000223653	TF binding region
ENSG00000153904	Chromatin interaction
ENSG00000272691	Chromatin interaction
ENSG00000097096	Chromatin interaction
ENSG00000162642	Chromatin interaction
ENSG00000142871	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11161563	1.00[CEU][hapmap];0.84[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11161566	0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs11161569	0.90[ASN][1000 genomes]
rs11161572	1.00[CEU][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11370	0.90[ASN][1000 genomes]
rs12025860	0.93[ASN][1000 genomes]
rs12025898	0.95[ASN][1000 genomes]
rs12036224	1.00[CHB][hapmap];0.92[JPT][hapmap];0.95[ASN][1000 genomes]
rs12039980	0.94[ASN][1000 genomes]
rs12133263	1.00[CEU][hapmap];0.92[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12143319	0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs2735595	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3768235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55806921	0.83[EUR][1000 genomes]
rs6700749	1.00[CEU][hapmap];1.00[EUR][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	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv830459	chr1:85589585-85786311	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85725400-85741000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:85726000-85741000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:85726000-85741400	Weak transcription	Gastric	stomach
4	chr1:85727200-85741400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:85732600-85741000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:85735000-85741400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:85735000-85741400	Weak transcription	Pancreas	Pancrea
8	chr1:85735600-85741400	Weak transcription	Lung	lung
9	chr1:85736800-85741000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr1:85737000-85741000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:85737800-85741200	Weak transcription	Placenta	Placenta
12	chr1:85739000-85741000	Flanking Active TSS	HUVEC	blood vessel
13	chr1:85739200-85743000	Active TSS	Psoas Muscle	Psoas
14	chr1:85739400-85741000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:85739400-85741200	Flanking Active TSS	Osteobl	bone
16	chr1:85739600-85741000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr1:85739600-85741000	Enhancers	Cortex derived primary cultured neurospheres	brain
18	chr1:85739600-85741200	Weak transcription	Fetal Muscle Trunk	muscle
19	chr1:85739600-85741200	Active TSS	HSMMtube	muscle
20	chr1:85739600-85741400	Weak transcription	Spleen	Spleen
21	chr1:85739600-85741600	Flanking Active TSS	Rectal Smooth Muscle	rectum
22	chr1:85739600-85741800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr1:85739600-85742200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr1:85739800-85741000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
25	chr1:85739800-85741200	Enhancers	Small Intestine	intestine
26	chr1:85739800-85741400	Flanking Active TSS	Duodenum Mucosa	Duodenum
27	chr1:85739800-85741800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:85739800-85742800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr1:85740000-85741000	Enhancers	Brain Hippocampus Middle	brain
30	chr1:85740000-85741000	Flanking Active TSS	NH-A	brain
31	chr1:85740000-85741200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr1:85740000-85741600	Flanking Active TSS	Dnd41	blood
33	chr1:85740000-85741800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
34	chr1:85740200-85741000	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:85740200-85741000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
36	chr1:85740200-85741000	Enhancers	Fetal Stomach	stomach
37	chr1:85740200-85741000	Enhancers	Thymus	Thymus
38	chr1:85740200-85741200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
39	chr1:85740200-85741200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
40	chr1:85740200-85741200	Enhancers	Fetal Thymus	thymus
41	chr1:85740200-85741600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr1:85740200-85741600	Flanking Active TSS	Hela-S3	cervix
43	chr1:85740200-85741800	Flanking Active TSS	Primary B cells from cord blood	blood
44	chr1:85740200-85743200	Active TSS	Colonic Mucosa	Colon
45	chr1:85740400-85741000	Transcr. at gene 5' and 3'	K562	blood
46	chr1:85740400-85741200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
47	chr1:85740400-85741400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr1:85740400-85741800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
49	chr1:85740400-85742400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:85740400-85742600	Active TSS	GM12878-XiMat	blood

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