Variant report

Variant	rs12416304
Chromosome Location	chr10:45492223-45492224
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	CEBPB	chr10:45491988-45492411	HepG2	liver:	n/a	chr10:45492220-45492231
2	POLR2A	chr10:45491567-45492568	HepG2	liver:	n/a	n/a
3	NFIC	chr10:45491155-45492366	HepG2	liver:	n/a	n/a
4	POLR2A	chr10:45491442-45492320	U87	brain:	n/a	n/a
5	POLR2A	chr10:45491166-45492604	HepG2	liver:	n/a	n/a
6	MAX	chr10:45491348-45492410	HUVEC	blood vessel:	n/a	chr10:45491936-45491947 chr10:45491642-45491651
7	POLR2A	chr10:45491762-45492332	GM12891	blood:	n/a	n/a
8	ARID3A	chr10:45491249-45492276	HepG2	liver:	n/a	n/a
9	POLR2A	chr10:45492144-45492262	H1-hESC	embryonic stem cell:	n/a	n/a
10	MXI1	chr10:45491260-45492341	HepG2	liver:	n/a	n/a
11	POLR2A	chr10:45491455-45492568	HL-60	blood:	n/a	n/a
12	POLR2A	chr10:45491596-45492489	GM12878	blood:	n/a	n/a
13	POLR2A	chr10:45491546-45492254	U87	brain:	n/a	n/a
14	HEY1	chr10:45491180-45492421	HepG2	liver:	n/a	n/a
15	EP300	chr10:45491134-45492251	HepG2	liver:	n/a	n/a
16	POLR2A	chr10:45492221-45492309	ProgFib	skin:	n/a	n/a
17	MAX	chr10:45491087-45492506	HepG2	liver:	n/a	chr10:45491936-45491947 chr10:45491642-45491651
18	MYBL2	chr10:45491106-45492292	HepG2	liver:	n/a	n/a
19	POLR2A	chr10:45490763-45493058	HepG2	liver:	n/a	n/a
20	POLR2A	chr10:45491199-45493109	HUVEC	blood vessel:	n/a	n/a
21	FOSL2	chr10:45491239-45492430	HepG2	liver:	n/a	chr10:45492170-45492181
22	POLR2A	chr10:45491508-45492368	HL-60	blood:	n/a	n/a
23	SP1	chr10:45491159-45492361	HepG2	liver:	n/a	n/a
24	POLR2A	chr10:45491247-45492342	HUVEC	blood vessel:	n/a	n/a
25	POLR2A	chr10:45492158-45492316	HepG2	liver:	n/a	n/a
26	FOXA1	chr10:45491200-45492302	HepG2	liver:	n/a	n/a
27	POLR2A	chr10:45491496-45492381	HepG2	liver:	n/a	n/a
28	POLR2A	chr10:45489983-45493423	GM12878	blood:	n/a	n/a
29	POLR2A	chr10:45490674-45493096	HepG2	liver:	n/a	n/a
30	MYBL2	chr10:45491126-45492256	HepG2	liver:	n/a	n/a
31	FOXA1	chr10:45491133-45492245	HepG2	liver:	n/a	n/a
32	POLR2A	chr10:45491527-45492351	HepG2	liver:	n/a	n/a
33	BHLHE40	chr10:45491341-45492384	HepG2	liver:	n/a	chr10:45491937-45491946 chr10:45491935-45491948 chr10:45491937-45491946 chr10:45491938-45491947 chr10:45491931-45491952
34	MAX	chr10:45490675-45492276	NB4	blood:	n/a	chr10:45491936-45491947 chr10:45491642-45491651
35	HEY1	chr10:45491517-45492304	HepG2	liver:	n/a	n/a
36	JUN	chr10:45491278-45492251	HUVEC	blood vessel:	n/a	chr10:45492170-45492181

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:45428885..45431662-chr10:45490818..45493446,2	K562	blood:
2	chr10:45484647..45486660-chr10:45491733..45494393,2	MCF-7	breast:

Variant related genes	Relation type
ZNF22	TF binding region
ENSG00000107551	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs17157326	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2274885	0.81[AMR][1000 genomes]
rs3814569	0.84[AMR][1000 genomes]
rs4450127	0.89[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4948650	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4948939	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831846	chr10:45322236-45556370	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv831848	chr10:45490176-45667670	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:45478800-45495800	Weak transcription	HMEC	breast
2	chr10:45482400-45495600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr10:45484200-45494200	Enhancers	Right Atrium	heart
4	chr10:45484600-45494200	Enhancers	Ovary	ovary
5	chr10:45485200-45493600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr10:45486000-45495600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr10:45486000-45495600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr10:45487200-45495600	Weak transcription	Brain Germinal Matrix	brain
9	chr10:45487200-45496200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr10:45487400-45495600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr10:45487800-45495800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr10:45488200-45496000	Enhancers	Placenta	Placenta
13	chr10:45488400-45495800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr10:45488800-45492600	Enhancers	Gastric	stomach
15	chr10:45488800-45492800	Enhancers	NHLF	lung
16	chr10:45488800-45493000	Enhancers	Esophagus	oesophagus
17	chr10:45488800-45495600	Enhancers	Primary hematopoietic stem cells	blood
18	chr10:45489000-45492800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr10:45489000-45493200	Enhancers	NHDF-Ad	bronchial
20	chr10:45489200-45492400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr10:45489200-45492600	Enhancers	Muscle Satellite Cultured Cells	--
22	chr10:45489200-45493600	Enhancers	HUVEC	blood vessel
23	chr10:45489200-45494200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr10:45489200-45494200	Enhancers	Lung	lung
25	chr10:45489200-45495200	Enhancers	Dnd41	blood
26	chr10:45489200-45495600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr10:45489400-45495200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr10:45489400-45495400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr10:45489600-45495800	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr10:45489800-45492600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr10:45489800-45493400	Enhancers	Primary hematopoietic stem cells short term culture	blood
32	chr10:45490000-45492600	Enhancers	Primary T cells from cord blood	blood
33	chr10:45490000-45493200	Enhancers	Colon Smooth Muscle	Colon
34	chr10:45490000-45493600	Enhancers	Pancreas	Pancrea
35	chr10:45490000-45494000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr10:45490000-45495000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr10:45490000-45495600	Weak transcription	Fetal Brain Female	brain
38	chr10:45490000-45496000	Enhancers	Right Ventricle	heart
39	chr10:45490200-45492400	Enhancers	Primary T cells fromperipheralblood	blood
40	chr10:45490200-45492800	Enhancers	Stomach Mucosa	stomach
41	chr10:45490200-45493000	Enhancers	Fetal Thymus	thymus
42	chr10:45490200-45493200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr10:45490200-45493400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr10:45490200-45494200	Enhancers	Psoas Muscle	Psoas
45	chr10:45490200-45495400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr10:45490400-45492600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr10:45490400-45492600	Enhancers	Thymus	Thymus
48	chr10:45490400-45493200	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr10:45490400-45493400	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr10:45490400-45493400	Weak transcription	HUES48 Cell Line	embryonic stem cell

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