Variant report

Variant	rs11189342
Chromosome Location	chr10:99473666-99473667
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:180)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:180 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:99472861-99474882	MCF-7	breast:	n/a	n/a
2	YY1	chr10:99473138-99473679	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr10:99473664-99474129	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr10:99473058-99475334	H1-hESC	embryonic stem cell:	n/a	n/a
5	CCNT2	chr10:99473507-99474389	K562	blood:	n/a	n/a
6	E2F6	chr10:99473529-99474893	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr10:99473078-99474878	GM18505	blood:	n/a	n/a
8	POLR2A	chr10:99472984-99475112	ProgFib	skin:	n/a	n/a
9	POLR2A	chr10:99473271-99474214	K562	blood:	n/a	n/a
10	POLR2A	chr10:99473161-99474873	HEK293	kidney:	n/a	n/a
11	MAX	chr10:99473092-99474975	SK-N-SH	brain:	n/a	n/a
12	MAX	chr10:99472582-99475098	HCT-116	colon:	n/a	n/a
13	YY1	chr10:99473443-99473783	GM12891	blood:	n/a	n/a
14	BHLHE40	chr10:99473517-99474088	K562	blood:	n/a	n/a
15	MAZ	chr10:99473659-99474172	GM12878	blood:	n/a	n/a
16	MAX	chr10:99473648-99474462	A549	lung:	n/a	n/a
17	CHD1	chr10:99473425-99475908	IMR90	lung:	n/a	n/a
18	E2F6	chr10:99473393-99474572	K562	blood:	n/a	n/a
19	MAX	chr10:99473539-99474117	K562	blood:	n/a	n/a
20	TCF7L2	chr10:99473437-99474954	HCT-116	colon:	n/a	n/a
21	POLR2A	chr10:99473574-99474479	GM12878	blood:	n/a	n/a
22	YY1	chr10:99473431-99474255	ECC-1	luminal epithelium:	n/a	n/a
23	SIN3AK20	chr10:99472978-99474860	PANC-1	pancreas:	n/a	n/a
24	MAX	chr10:99473310-99474905	MCF-7	breast:	n/a	n/a
25	MYC	chr10:99473436-99474841	MCF10A-Er-Src	breast:	n/a	n/a
26	MXI1	chr10:99472608-99474975	SK-N-SH	brain:	n/a	n/a
27	POLR2A	chr10:99473050-99474816	Hela-S3	cervix:	n/a	n/a
28	TAF1	chr10:99473666-99474858	MCF-7	breast:	n/a	n/a
29	USF1	chr10:99473651-99474216	ECC-1	luminal epithelium:	n/a	n/a
30	TBP	chr10:99473318-99474212	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr10:99473613-99474532	GM12878	blood:	n/a	n/a
32	POLR2A	chr10:99473426-99474028	K562	blood:	n/a	n/a
33	E2F1	chr10:99473031-99474540	Hela-S3	cervix:	n/a	chr10:99473079-99473091
34	TCF12	chr10:99473459-99474552	ECC-1	luminal epithelium:	n/a	n/a
35	POLR2A	chr10:99473264-99474877	NB4	blood:	n/a	n/a
36	MAX	chr10:99472952-99474910	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr10:99473189-99474896	U87	brain:	n/a	n/a
38	HA-E2F1	chr10:99473021-99474637	Hela-S3	cervix:	n/a	chr10:99473079-99473091
39	MAX	chr10:99472699-99475009	A549	lung:	n/a	n/a
40	MYC	chr10:99473448-99474318	K562	blood:	n/a	n/a
41	POLR2A	chr10:99473655-99474904	SK-N-SH	brain:	n/a	n/a
42	POLR2A	chr10:99473117-99474478	GM15510	blood:	n/a	n/a
43	EGR1	chr10:99473198-99473789	K562	blood:	n/a	chr10:99473603-99473617
44	POLR2A	chr10:99473583-99474211	K562	blood:	n/a	n/a
45	MAX	chr10:99473479-99474414	ECC-1	luminal epithelium:	n/a	n/a
46	CREB1	chr10:99473661-99474670	A549	lung:	n/a	n/a
47	TAF1	chr10:99473652-99474132	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr10:99473134-99474581	H1-neurons	neurons:	n/a	n/a
49	YY1	chr10:99473167-99474309	ECC-1	luminal epithelium:	n/a	n/a
50	YY1	chr10:99473401-99474158	GM12892	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:99471547..99474270-chr10:99495747..99497533,2	K562	blood:
2	chr10:99472472..99476089-chr10:99494153..99498366,9	MCF-7	breast:
3	chr10:99443080..99453237-chr10:99471420..99478243,12	MCF-7	breast:
4	chr10:99472128..99477527-chr10:99495091..99498402,11	MCF-7	breast:
5	chr10:99442762..99448311-chr10:99470830..99475549,8	MCF-7	breast:
6	chr10:99473490..99474131-chr17:41444618..41445483,3	Hela-S3	cervix:
7	chr10:99257277..99258845-chr10:99472952..99474913,2	MCF-7	breast:
8	chr10:99473151..99473931-chr16:89557220..89557802,2	Hela-S3	cervix:
9	chr10:99444910..99448624-chr10:99472151..99475238,4	K562	blood:

No data

Variant related genes	Relation type
MARVELD1	TF binding region
ENSG00000155256	Chromatin interaction
ENSG00000119986	Chromatin interaction
ENSG00000155229	Chromatin interaction
ENSG00000165886	Chromatin interaction
ENSG00000197912	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10748706	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12415272	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4919133	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4919135	0.82[ASN][1000 genomes]
rs6584148	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6584149	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7896853	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7900119	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7914697	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7915100	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1817777	chr10:99196035-99558169	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers 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 target site	66 gene(s)	inside rSNPs	diseases
2	esv3438921	chr10:99472487-99475335	Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv467441	chr10:99472710-99541104	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	nsv552026	chr10:99472710-99541104	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11189342	MARVELD1	cis	lung	GTEx
rs11189342	MARVELD1	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99472000-99474800	Active TSS	Duodenum Smooth Muscle	Duodenum
2	chr10:99472600-99473800	Enhancers	GM12878-XiMat	blood
3	chr10:99472600-99474600	Active TSS	Fetal Brain Female	brain
4	chr10:99472600-99474800	Active TSS	Fetal Lung	lung
5	chr10:99472600-99475000	Active TSS	Brain Angular Gyrus	brain
6	chr10:99472600-99475000	Active TSS	Fetal Kidney	kidney
7	chr10:99472800-99474000	Flanking Active TSS	Primary hematopoietic stem cells	blood
8	chr10:99472800-99474000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr10:99472800-99474200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr10:99472800-99474400	Flanking Active TSS	Adipose Nuclei	Adipose
11	chr10:99472800-99474400	Active TSS	Colonic Mucosa	Colon
12	chr10:99472800-99474800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr10:99472800-99474800	Active TSS	Brain Substantia Nigra	brain
14	chr10:99473000-99473800	Flanking Bivalent TSS/Enh	Thymus	Thymus
15	chr10:99473000-99474000	Transcr. at gene 5' and 3'	Right Atrium	heart
16	chr10:99473000-99474600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr10:99473000-99474600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
18	chr10:99473000-99474800	Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr10:99473000-99474800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr10:99473000-99474800	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr10:99473000-99474800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr10:99473000-99474800	Active TSS	Brain Anterior Caudate	brain
23	chr10:99473000-99474800	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr10:99473000-99474800	Active TSS	Ovary	ovary
25	chr10:99473000-99474800	Active TSS	HSMM	muscle
26	chr10:99473000-99474800	Active TSS	NHLF	lung
27	chr10:99473000-99474800	Active TSS	Osteobl	bone
28	chr10:99473000-99475000	Active TSS	ES-I3 Cell Line	embryonic stem cell
29	chr10:99473000-99475000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr10:99473000-99475000	Active TSS	HUES48 Cell Line	embryonic stem cell
31	chr10:99473000-99475000	Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr10:99473000-99475000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr10:99473000-99475000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
34	chr10:99473000-99475000	Active TSS	Colon Smooth Muscle	Colon
35	chr10:99473000-99475000	Active TSS	Placenta Amnion	Placenta Amnion
36	chr10:99473000-99475200	Active TSS	HUES64 Cell Line	embryonic stem cell
37	chr10:99473000-99475200	Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr10:99473000-99475200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr10:99473000-99475200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr10:99473000-99475200	Active TSS	Brain Inferior Temporal Lobe	brain
41	chr10:99473000-99475400	Active TSS	H9 Cell Line	embryonic stem cell
42	chr10:99473000-99475400	Active TSS	Psoas Muscle	Psoas
43	chr10:99473000-99475400	Active TSS	NHDF-Ad	bronchial
44	chr10:99473000-99475600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr10:99473000-99475800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
46	chr10:99473000-99476200	Active TSS	Aorta	Aorta
47	chr10:99473200-99473800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr10:99473200-99473800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr10:99473200-99473800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
50	chr10:99473200-99473800	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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