Variant report

Variant	rs7922577
Chromosome Location	chr10:20104426-20104427
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	MAX	chr10:20104289-20105332	H1-hESC	embryonic stem cell:	n/a	n/a
2	EP300	chr10:20104267-20104817	H1-hESC	embryonic stem cell:	n/a	chr10:20104532-20104548
3	YY1	chr10:20104405-20105112	H1-hESC	embryonic stem cell:	n/a	chr10:20104487-20104498 chr10:20104880-20104891 chr10:20104812-20104821
4	TAF1	chr10:20104307-20106910	H1-hESC	embryonic stem cell:	n/a	n/a
5	MYC	chr10:20104425-20105280	MCF-7	breast:	n/a	n/a
6	TBP	chr10:20104312-20106062	H1-hESC	embryonic stem cell:	n/a	n/a
7	ZNF143	chr10:20104121-20105172	H1-hESC	embryonic stem cell:	n/a	n/a
8	ELF1	chr10:20104126-20104566	MCF-7	breast:	n/a	chr10:20104486-20104495
9	POLR2A	chr10:20104290-20106963	GM18951	blood:	n/a	n/a
10	POLR2A	chr10:20103964-20106407	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr10:20104425-20106051	MCF-7	breast:	n/a	n/a
12	EGR1	chr10:20104075-20105200	H1-hESC	embryonic stem cell:	n/a	chr10:20104830-20104840 chr10:20104456-20104466 chr10:20105151-20105161 chr10:20104457-20104466
13	MXI1	chr10:20104416-20104668	H1-hESC	embryonic stem cell:	n/a	n/a
14	SIN3AK20	chr10:20104232-20107072	MCF-7	breast:	n/a	n/a
15	KAP1	chr10:20104258-20104778	HEK293	kidney:	n/a	n/a
16	POLR2A	chr10:20104372-20106075	HEK293	kidney:	n/a	n/a
17	ZNF263	chr10:20104105-20107572	HEK293-T-REx	kidney:	n/a	chr10:20105077-20105086 chr10:20105731-20105740 chr10:20105030-20105051 chr10:20105495-20105504 chr10:20105032-20105041 chr10:20106472-20106481 chr10:20106475-20106484 chr10:20105084-20105093
18	MAX	chr10:20104387-20104667	H1-hESC	embryonic stem cell:	n/a	n/a
19	YY1	chr10:20104423-20105254	H1-hESC	embryonic stem cell:	n/a	chr10:20104487-20104498 chr10:20104880-20104891 chr10:20104812-20104821
20	MAZ	chr10:20104183-20105861	IMR90	lung:	n/a	n/a
21	POLR2A	chr10:20104318-20106280	H1-hESC	embryonic stem cell:	n/a	n/a
22	SP4	chr10:20104363-20104677	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr10:20104182-20106604	MCF10A-Er-Src	breast:	n/a	n/a
24	POLR2A	chr10:20104301-20105596	PFSK-1	brain:	n/a	n/a
25	POLR2A	chr10:20104299-20106151	H1-neurons	neurons:	n/a	n/a
26	TAF7	chr10:20104398-20105292	H1-hESC	embryonic stem cell:	n/a	n/a
27	SIN3AK20	chr10:20104398-20105125	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr10:20104341-20105317	H1-hESC	embryonic stem cell:	n/a	n/a
29	RAD21	chr10:20104247-20106695	IMR90	lung:	n/a	chr10:20104323-20104332 chr10:20104759-20104771
30	POLR2A	chr10:20104219-20106074	SK-N-MC	brain:	n/a	n/a
31	TAF1	chr10:20104335-20104964	H1-hESC	embryonic stem cell:	n/a	n/a
32	MAX	chr10:20104345-20106125	ECC-1	luminal epithelium:	n/a	n/a
33	ATF2	chr10:20104385-20104787	H1-hESC	embryonic stem cell:	n/a	n/a
34	CTBP2	chr10:20104368-20107024	H1-hESC	embryonic stem cell:	n/a	n/a
35	CHD1	chr10:20104302-20104671	H1-hESC	embryonic stem cell:	n/a	chr10:20104640-20104650
36	FOXP2	chr10:20104403-20105295	PFSK-1	brain:	n/a	n/a
37	POLR2A	chr10:20104200-20107039	H1-hESC	embryonic stem cell:	n/a	n/a
38	ZBTB7A	chr10:20104317-20105329	ECC-1	luminal epithelium:	n/a	chr10:20104638-20104645
39	MAX	chr10:20104337-20105246	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr10:20104390-20106141	H1-neurons	neurons:	n/a	n/a
41	NANOG	chr10:20104325-20105086	H1-hESC	embryonic stem cell:	n/a	n/a
42	ZBTB7A	chr10:20104237-20105065	ECC-1	luminal epithelium:	n/a	chr10:20104638-20104645
43	MYC	chr10:20104375-20104678	MCF10A-Er-Src	breast:	n/a	n/a
44	CEBPB	chr10:20104217-20104660	H1-hESC	embryonic stem cell:	n/a	n/a
45	RAD21	chr10:20104253-20107113	H1-hESC	embryonic stem cell:	n/a	chr10:20106920-20106930 chr10:20104323-20104332 chr10:20104759-20104771
46	RAD21	chr10:20104221-20105802	H1-hESC	embryonic stem cell:	n/a	chr10:20104323-20104332 chr10:20104759-20104771
47	MXI1	chr10:20103634-20107079	IMR90	lung:	n/a	n/a
48	CHD2	chr10:20104354-20105051	H1-hESC	embryonic stem cell:	n/a	chr10:20104691-20104701 chr10:20104640-20104650
49	SIN3A	chr10:20104096-20107647	H1-hESC	embryonic stem cell:	n/a	chr10:20107381-20107391 chr10:20106643-20106652 chr10:20104768-20104781
50	HA-E2F1	chr10:20104176-20106077	MCF-7	breast:	n/a	chr10:20105998-20106008 chr10:20104484-20104494 chr10:20104812-20104821

Variant related genes	Relation type
PLXDC2	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs16919374	0.83[ASN][1000 genomes]
rs1977538	0.88[EUR][1000 genomes]
rs2478143	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2481935	0.81[ASN][1000 genomes]
rs372542	0.86[EUR][1000 genomes]
rs391559	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4748611	0.98[EUR][1000 genomes]
rs7076946	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs989767	0.91[MEX][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	nsv1049295	chr10:19740296-20509036	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	esv34306	chr10:19777069-20117944	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv1044794	chr10:20010269-20391329	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv540510	chr10:20010269-20391329	Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1038966	chr10:20010469-20391190	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv540511	chr10:20010469-20391190	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1037055	chr10:20010469-20651965	Enhancers Bivalent/Poised TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv540512	chr10:20010469-20651965	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7922577	C10orf67	cis	parietal	SCAN

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:20103400-20106400	Active TSS	Stomach Smooth Muscle	stomach
2	chr10:20103400-20109000	Active TSS	Brain Anterior Caudate	brain
3	chr10:20103400-20110200	Active TSS	Brain Hippocampus Middle	brain
4	chr10:20103600-20105600	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr10:20103600-20107600	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr10:20103800-20105400	Active TSS	Skeletal Muscle Female	skeletal muscle
7	chr10:20103800-20106200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr10:20103800-20106400	Active TSS	Duodenum Mucosa	Duodenum
9	chr10:20103800-20107200	Active TSS	Rectal Mucosa Donor 31	rectum
10	chr10:20103800-20107400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr10:20103800-20107800	Active TSS	Colon Smooth Muscle	Colon
12	chr10:20103800-20108000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
13	chr10:20103800-20108000	Active TSS	Rectal Smooth Muscle	rectum
14	chr10:20103800-20108600	Active TSS	H9 Cell Line	embryonic stem cell
15	chr10:20103800-20108600	Active TSS	Brain Inferior Temporal Lobe	brain
16	chr10:20103800-20108600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
17	chr10:20103800-20108800	Active TSS	Brain Angular Gyrus	brain
18	chr10:20103800-20108800	Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr10:20103800-20109000	Active TSS	Brain Cingulate Gyrus	brain
20	chr10:20103800-20109000	Active TSS	HSMMtube	muscle
21	chr10:20104000-20104600	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr10:20104000-20104600	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
23	chr10:20104000-20104600	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr10:20104000-20104600	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
25	chr10:20104000-20104600	Flanking Active TSS	HMEC	breast
26	chr10:20104000-20104800	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
27	chr10:20104000-20104800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr10:20104000-20105600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr10:20104000-20105600	Active TSS	Fetal Intestine Large	intestine
30	chr10:20104000-20105600	Active TSS	Fetal Muscle Trunk	muscle
31	chr10:20104000-20106200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
32	chr10:20104000-20106400	Active TSS	Fetal Muscle Leg	muscle
33	chr10:20104000-20107400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr10:20104000-20107400	Active TSS	HUES48 Cell Line	embryonic stem cell
35	chr10:20104000-20107400	Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr10:20104000-20107400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr10:20104000-20107600	Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr10:20104000-20107600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr10:20104000-20107600	Active TSS	Right Ventricle	heart
40	chr10:20104000-20107600	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
41	chr10:20104000-20107800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
42	chr10:20104000-20107800	Active TSS	Pancreatic Islets	Pancreatic Islet
43	chr10:20104000-20107800	Bivalent/Poised TSS	Osteobl	bone
44	chr10:20104000-20108000	Active TSS	HUES64 Cell Line	embryonic stem cell
45	chr10:20104000-20108000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr10:20104000-20108000	Flanking Active TSS	Adipose Nuclei	Adipose
47	chr10:20104000-20108000	Active TSS	Aorta	Aorta
48	chr10:20104000-20108000	Active TSS	Psoas Muscle	Psoas
49	chr10:20104000-20108200	Active TSS	H1 Cell Line	embryonic stem cell
50	chr10:20104000-20108200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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