Variant report

Variant	rs531200388
Chromosome Location	chr1:190447071-190447072
allele	A/C
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	POLR2A	chr1:190446856-190447801	H1-neurons	neurons:	n/a	n/a
2	REST	chr1:190446596-190448409	H1-neurons	neurons:	n/a	chr1:190447480-190447493 chr1:190448080-190448087 chr1:190447477-190447490 chr1:190447462-190447480 chr1:190447339-190447352 chr1:190447792-190447805 chr1:190447332-190447345
3	MAX	chr1:190446891-190447358	H1-hESC	embryonic stem cell:	n/a	n/a
4	GATA2	chr1:190446768-190448262	SH-SY5Y	brain:	n/a	n/a
5	CTCF	chr1:190447060-190447210	BE2_C	brain:	n/a	n/a
6	TCF7L2	chr1:190446979-190448068	HCT-116	colon:	n/a	n/a
7	FOS	chr1:190446935-190447123	MCF10A-Er-Src	breast:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RGS18-5	chr1:190446965-190447761	NONHSAT008497

Variant related genes	Relation type
ENSG00000241505	TF binding region
BRINP3	TF binding region
ENSG00000237457	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932040	chr1:190005334-190914580	Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv872758	chr1:190351677-190510003	Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv872760	chr1:190377988-190577336	Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv872761	chr1:190389741-190485034	Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv872762	chr1:190389741-190510003	Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Strong transcription Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv872763	chr1:190389741-190531642	Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv872764	chr1:190399946-190531642	Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	nsv872765	chr1:190418653-190464647	Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv466750	chr1:190433413-190496007	Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	nsv548551	chr1:190433413-190496007	Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv466761	chr1:190433413-190545283	Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv548552	chr1:190433413-190545283	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv466772	chr1:190446253-190492280	Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
14	nsv548553	chr1:190446253-190492280	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:190440000-190448800	Active TSS	Duodenum Mucosa	Duodenum
2	chr1:190440200-190448800	Active TSS	Fetal Intestine Large	intestine
3	chr1:190440800-190448600	Active TSS	Rectal Mucosa Donor 31	rectum
4	chr1:190440800-190448800	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr1:190441200-190448600	Active TSS	Fetal Intestine Small	intestine
6	chr1:190441200-190448600	Active TSS	Right Atrium	heart
7	chr1:190443000-190449600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
8	chr1:190444800-190447200	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
9	chr1:190445000-190447600	Active TSS	Brain Angular Gyrus	brain
10	chr1:190445200-190447200	Weak transcription	Gastric	stomach
11	chr1:190445200-190449000	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr1:190445400-190447200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:190445400-190447200	Weak transcription	Pancreas	Pancrea
14	chr1:190445400-190447200	Weak transcription	NHLF	lung
15	chr1:190446200-190448800	Active TSS	Brain Germinal Matrix	brain
16	chr1:190446200-190449600	Active TSS	Brain Anterior Caudate	brain
17	chr1:190446200-190450000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr1:190446600-190447200	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
19	chr1:190446600-190447200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
20	chr1:190446600-190447200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:190446600-190447600	Active TSS	Colonic Mucosa	Colon
22	chr1:190446600-190447800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr1:190446600-190447800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
24	chr1:190446600-190448000	Bivalent/Poised TSS	Brain Substantia Nigra	brain
25	chr1:190446600-190448400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr1:190446800-190447200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:190446800-190447200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
28	chr1:190446800-190447200	Flanking Active TSS	Fetal Brain Female	brain
29	chr1:190446800-190447200	Flanking Active TSS	Fetal Heart	heart
30	chr1:190446800-190447200	Active TSS	Fetal Stomach	stomach
31	chr1:190446800-190447200	Active TSS	Psoas Muscle	Psoas
32	chr1:190446800-190447200	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr1:190446800-190447400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
34	chr1:190446800-190447400	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
35	chr1:190446800-190447600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
36	chr1:190446800-190447800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
37	chr1:190446800-190448400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr1:190446800-190448400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr1:190446800-190448400	Active TSS	Rectal Smooth Muscle	rectum
40	chr1:190447000-190447200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
41	chr1:190447000-190447200	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr1:190447000-190447200	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr1:190447000-190447200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr1:190447000-190447200	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
45	chr1:190447000-190447200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr1:190447000-190447200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
47	chr1:190447000-190447200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:190447000-190447200	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:190447000-190447200	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr1:190447000-190447200	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose

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