Variant report

Variant	rs6662684
Chromosome Location	chr1:10490789-10490790
allele	C/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	EGR1	chr1:10490088-10491191	HCT-116	colon:	n/a	chr1:10490750-10490759 chr1:10490721-10490735 chr1:10490350-10490360
2	ZNF143	chr1:10490247-10491202	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr1:10490174-10491199	GM19193	blood:	n/a	n/a
4	POLR2A	chr1:10490008-10491366	GM12878	blood:	n/a	n/a
5	POLR2A	chr1:10490262-10491087	HCT-116	colon:	n/a	n/a
6	CHD2	chr1:10490179-10491510	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:10490088-10491011	K562	blood:	n/a	n/a
8	CTCF	chr1:10490680-10490830	Hela-S3	cervix:	n/a	chr1:10490696-10490709
9	JUND	chr1:10490031-10491147	K562	blood:	n/a	n/a
10	POLR2A	chr1:10490251-10491230	U87	brain:	n/a	n/a
11	SIN3AK20	chr1:10490728-10490976	A549	lung:	n/a	n/a
12	MYC	chr1:10490327-10491051	MCF10A-Er-Src	breast:	n/a	n/a
13	UBTF	chr1:10490195-10491528	K562	blood:	n/a	n/a
14	CHD2	chr1:10490257-10490930	K562	blood:	n/a	n/a
15	FOXM1	chr1:10490105-10491180	GM12878	blood:	n/a	n/a
16	RFX5	chr1:10490279-10490903	K562	blood:	n/a	chr1:10490792-10490807 chr1:10490792-10490807 chr1:10490792-10490807
17	TCF12	chr1:10490139-10491395	ECC-1	luminal epithelium:	n/a	n/a
18	EGR1	chr1:10490164-10490899	K562	blood:	n/a	chr1:10490750-10490759 chr1:10490721-10490735 chr1:10490350-10490360
19	MAX	chr1:10489978-10491108	HUVEC	blood vessel:	n/a	chr1:10490255-10490262
20	TBL1XR1	chr1:10490105-10491547	K562	blood:	n/a	n/a
21	YY1	chr1:10490226-10491017	K562	blood:	n/a	chr1:10490696-10490710 chr1:10490821-10490835 chr1:10490692-10490703
22	POLR2A	chr1:10490001-10491062	GM12891	blood:	n/a	n/a
23	BCLAF1	chr1:10490759-10491165	GM12878	blood:	n/a	n/a
24	POLR2A	chr1:10490368-10491111	HepG2	liver:	n/a	n/a
25	ZBTB7A	chr1:10490131-10491135	ECC-1	luminal epithelium:	n/a	chr1:10490528-10490535 chr1:10490430-10490439
26	SIN3AK20	chr1:10490052-10491405	PANC-1	pancreas:	n/a	n/a
27	POLR2A	chr1:10490232-10491258	HEK293	kidney:	n/a	n/a
28	POLR2A	chr1:10490088-10491133	PANC-1	pancreas:	n/a	n/a
29	MAX	chr1:10490265-10491360	Hela-S3	cervix:	n/a	n/a
30	ATF2	chr1:10490155-10491320	H1-hESC	embryonic stem cell:	n/a	n/a
31	HEY1	chr1:10490148-10491053	K562	blood:	n/a	n/a
32	SPI1	chr1:10490697-10490957	K562	blood:	n/a	n/a
33	TAL1	chr1:10490332-10491209	K562	blood:	n/a	n/a
34	ATF2	chr1:10490050-10491090	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr1:10490130-10491094	GM12878	blood:	n/a	n/a
36	POLR2A	chr1:10490381-10490931	K562	blood:	n/a	n/a
37	POLR2A	chr1:10490426-10491060	MCF10A-Er-Src	breast:	n/a	n/a
38	E2F6	chr1:10490253-10491133	K562	blood:	n/a	chr1:10490750-10490759 chr1:10490696-10490706 chr1:10490431-10490440 chr1:10490495-10490506
39	SPI1	chr1:10490700-10491015	GM12891	blood:	n/a	n/a
40	CTCF	chr1:10490780-10490930	HAc	cerebellar:	n/a	n/a
41	CHD1	chr1:10490254-10491126	GM12878	blood:	n/a	n/a
42	POLR2A	chr1:10490195-10491350	Hela-S3	cervix:	n/a	n/a
43	ELK1	chr1:10490257-10491041	GM12878	blood:	n/a	n/a
44	MYC	chr1:10490137-10491213	K562	blood:	n/a	chr1:10490255-10490262
45	ELF1	chr1:10490241-10491013	K562	blood:	n/a	n/a
46	FOXM1	chr1:10490162-10491077	GM12878	blood:	n/a	n/a
47	E2F4	chr1:10490213-10491409	K562	blood:	n/a	chr1:10490750-10490759 chr1:10490696-10490706 chr1:10490431-10490440 chr1:10490495-10490506
48	POLR2A	chr1:10490083-10491658	HepG2	liver:	n/a	n/a
49	TBL1XR1	chr1:10490353-10491008	GM12878	blood:	n/a	n/a
50	POLR2A	chr1:10490363-10491048	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:10270585..10272249-chr1:10490197..10491890,2	K562	blood:
2	chr1:10473791..10476777-chr1:10490511..10492354,2	K562	blood:
3	chr1:10457794..10460664-chr1:10487844..10492697,5	K562	blood:
4	chr1:10490607..10494447-chr1:10532445..10535163,5	K562	blood:
5	chr1:10488008..10492443-chr1:10531123..10534892,8	K562	blood:
6	chr1:10490085..10492364-chr1:10508772..10511442,3	K562	blood:
7	chr1:10488905..10491611-chr1:10518532..10520834,2	MCF-7	breast:
8	chr1:10489993..10493018-chr1:10531254..10535234,5	MCF-7	breast:
9	chr1:10489448..10493967-chr1:10494423..10498103,7	K562	blood:
10	chr1:10002273..10004549-chr1:10490535..10492203,2	MCF-7	breast:
11	chr1:10457794..10461321-chr1:10487053..10491931,7	K562	blood:

Variant related genes	Relation type
APITD1	TF binding region
ENSG00000271989	TF binding region
APITD1-CORT	TF binding region
ENSG00000142657	Chromatin interaction
ENSG00000173614	Chromatin interaction
ENSG00000054523	Chromatin interaction
ENSG00000228150	Chromatin interaction
ENSG00000160049	Chromatin interaction
ENSG00000203469	Chromatin interaction
ENSG00000142655	Chromatin interaction
ENSG00000241563	Chromatin interaction
ENSG00000251503	Chromatin interaction
ENSG00000162441	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10436981	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11121572	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12126556	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12134590	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12745969	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35138970	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3828044	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs597441	0.81[EUR][1000 genomes]

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	esv2757722	chr1:10238070-10582554	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv2758920	chr1:10238070-10582554	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv817370	chr1:10305470-10697150	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1008021	chr1:10363794-10802633	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv2764192	chr1:10383734-10594186	Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv1003498	chr1:10445928-10607351	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv998731	chr1:10464176-10607351	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	esv3373675	chr1:10489565-10491863	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6662684	PGD	cis	Muscle Skeletal	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:10489800-10491400	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr1:10489800-10491400	Active TSS	Brain Germinal Matrix	brain
3	chr1:10489800-10491600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr1:10489800-10491600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
5	chr1:10490000-10491000	Active TSS	Fetal Brain Female	brain
6	chr1:10490000-10491400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr1:10490000-10491400	Active TSS	H9 Cell Line	embryonic stem cell
8	chr1:10490000-10491400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:10490000-10491600	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr1:10490000-10491600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:10490000-10491600	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr1:10490000-10491600	Flanking Active TSS	Primary hematopoietic stem cells	blood
13	chr1:10490000-10491600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr1:10490200-10490800	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
15	chr1:10490200-10491000	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
16	chr1:10490200-10491000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:10490200-10491200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:10490200-10491200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:10490200-10491200	Active TSS	Colon Smooth Muscle	Colon
20	chr1:10490200-10491200	Transcr. at gene 5' and 3'	Right Atrium	heart
21	chr1:10490200-10491400	Active TSS	Ovary	ovary
22	chr1:10490200-10491400	Active TSS	Thymus	Thymus
23	chr1:10490200-10491600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr1:10490200-10491600	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr1:10490200-10491600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
26	chr1:10490200-10491600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:10490200-10491600	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr1:10490200-10491800	Active TSS	HUES64 Cell Line	embryonic stem cell
29	chr1:10490200-10491800	Active TSS	iPS-18 Cell Line	embryonic stem cell
30	chr1:10490200-10491800	Active TSS	iPS-20b Cell Line	embryonic stem cell
31	chr1:10490200-10491800	Active TSS	A549	lung
32	chr1:10490400-10490800	Active TSS	Primary monocytes fromperipheralblood	blood
33	chr1:10490400-10490800	Active TSS	Primary neutrophils fromperipheralblood	blood
34	chr1:10490400-10490800	Active TSS	Primary hematopoietic stem cells short term culture	blood
35	chr1:10490400-10490800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
36	chr1:10490400-10490800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr1:10490400-10490800	Active TSS	Skeletal Muscle Female	skeletal muscle
38	chr1:10490400-10490800	Active TSS	Spleen	Spleen
39	chr1:10490400-10490800	Active TSS	HMEC	breast
40	chr1:10490400-10491000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr1:10490400-10491000	Active TSS	Primary B cells from peripheral blood	blood
42	chr1:10490400-10491000	Active TSS	Primary T cells fromperipheralblood	blood
43	chr1:10490400-10491000	Active TSS	Primary T helper naive cells fromperipheralblood	blood
44	chr1:10490400-10491000	Active TSS	Primary T helper cells fromperipheralblood	blood
45	chr1:10490400-10491000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr1:10490400-10491000	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
47	chr1:10490400-10491000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
48	chr1:10490400-10491000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr1:10490400-10491000	Active TSS	Adipose Nuclei	Adipose
50	chr1:10490400-10491000	Active TSS	Liver	Liver

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