Variant report

Variant	rs73858210
Chromosome Location	chr3:120628227-120628228
allele	A/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	REST	chr3:120626072-120628339	H1-neurons	neurons:	n/a	chr3:120627472-120627485 chr3:120627068-120627081 chr3:120627823-120627833 chr3:120627061-120627081 chr3:120627061-120627081 chr3:120627061-120627075 chr3:120627065-120627078 chr3:120627061-120627081
2	MXI1	chr3:120626257-120628925	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr3:120626384-120628307	H1-neurons	neurons:	n/a	n/a
4	SIN3A	chr3:120626338-120628654	H1-hESC	embryonic stem cell:	n/a	chr3:120627561-120627574 chr3:120627023-120627034 chr3:120627062-120627076 chr3:120627503-120627514 chr3:120627068-120627081
5	SIN3AK20	chr3:120628141-120628353	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
STXBP5L	TF binding region

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs3845851	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58611806	1.00[AMR][1000 genomes]
rs72966749	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73858217	1.00[AMR][1000 genomes]
rs7619589	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv869548	chr3:120320731-121076337	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv916869	chr3:120360281-120973169	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv829700	chr3:120469191-120675763	Strong transcription Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	esv3431805	chr3:120626112-120628860	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120626200-120628600	Active TSS	iPS-18 Cell Line	embryonic stem cell
2	chr3:120626200-120628800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
3	chr3:120626200-120629000	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr3:120626200-120630200	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr3:120626400-120628400	Active TSS	Brain Cingulate Gyrus	brain
6	chr3:120626400-120628400	Active TSS	Rectal Smooth Muscle	rectum
7	chr3:120626400-120628600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr3:120626400-120628600	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr3:120626400-120628600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:120626400-120628600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr3:120626400-120628600	Active TSS	Brain Anterior Caudate	brain
12	chr3:120626400-120628800	Active TSS	H1 Cell Line	embryonic stem cell
13	chr3:120626400-120628800	Active TSS	H9 Cell Line	embryonic stem cell
14	chr3:120626400-120628800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr3:120626400-120629200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr3:120626400-120630400	Active TSS	Brain Angular Gyrus	brain
17	chr3:120626400-120630400	Active TSS	Brain Inferior Temporal Lobe	brain
18	chr3:120626600-120628400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:120626600-120628600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr3:120626600-120628800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr3:120626600-120628800	Active TSS	Ovary	ovary
22	chr3:120626600-120629400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:120626800-120628400	Active TSS	Colon Smooth Muscle	Colon
24	chr3:120626800-120628400	Active TSS	Right Atrium	heart
25	chr3:120626800-120628600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr3:120626800-120628800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr3:120627000-120629000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr3:120627200-120628400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
29	chr3:120627200-120628800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
30	chr3:120627200-120628800	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
31	chr3:120627400-120628600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
32	chr3:120627400-120628600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
33	chr3:120627400-120628600	Enhancers	Placenta	Placenta
34	chr3:120627400-120628600	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
35	chr3:120627400-120628600	Active TSS	Stomach Smooth Muscle	stomach
36	chr3:120627400-120628800	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
37	chr3:120627600-120628600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
38	chr3:120627600-120628600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
39	chr3:120627600-120628600	Bivalent/Poised TSS	Colonic Mucosa	Colon
40	chr3:120627600-120628600	Active TSS	Right Ventricle	heart
41	chr3:120627600-120628600	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
42	chr3:120627800-120628400	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
43	chr3:120627800-120628400	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
44	chr3:120627800-120628400	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
45	chr3:120627800-120628600	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
46	chr3:120627800-120628600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
47	chr3:120627800-120628600	Bivalent Enhancer	Left Ventricle	heart
48	chr3:120627800-120628800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr3:120627800-120628800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
50	chr3:120627800-120629000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell

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