Variant report

Variant	rs2282333
Chromosome Location	chr1:46600274-46600275
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	RUNX3	chr1:46600208-46600840	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:46599617-46601123	K562	blood:	n/a	n/a
3	ATF2	chr1:46600239-46600790	GM12878	blood:	n/a	n/a
4	SPI1	chr1:46600237-46600544	GM12891	blood:	n/a	chr1:46600389-46600402 chr1:46600388-46600401 chr1:46600392-46600399
5	SPI1	chr1:46600087-46600659	GM12878	blood:	n/a	chr1:46600389-46600402 chr1:46600388-46600401 chr1:46600392-46600399
6	POLR2A	chr1:46597346-46600754	IMR90	lung:	n/a	n/a
7	GTF2F1	chr1:46600263-46601436	Hela-S3	cervix:	n/a	n/a
8	IKZF1	chr1:46600205-46600821	GM12878	blood:	n/a	chr1:46600362-46600374
9	NFIC	chr1:46600172-46600845	GM12878	blood:	n/a	n/a
10	SPI1	chr1:46600243-46600591	GM12891	blood:	n/a	chr1:46600389-46600402 chr1:46600388-46600401 chr1:46600392-46600399
11	MTA3	chr1:46597245-46601010	GM12878	blood:	n/a	n/a
12	RUNX3	chr1:46600213-46600946	GM12878	blood:	n/a	n/a
13	SPI1	chr1:46600265-46600581	GM12878	blood:	n/a	chr1:46600389-46600402 chr1:46600388-46600401 chr1:46600392-46600399

No.	Distal block	Cell Line	Cell type
1	chr1:46598178..46600574-chr1:46641246..46642770,2	K562	blood:
2	chr1:46597687..46601092-chr1:46685533..46687921,3	MCF-7	breast:
3	chr1:46592691..46601867-chr1:46642778..46650670,25	MCF-7	breast:
4	chr1:46593944..46606364-chr1:46632700..46654752,92	MCF-7	breast:
5	chr1:46590920..46606215-chr1:46630948..46642525,66	MCF-7	breast:
6	chr1:46595304..46602065-chr1:46660247..46665309,8	MCF-7	breast:
7	chr1:46598477..46601244-chr1:46712967..46714555,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TSPAN1-1	chr1:46600203-46600326	ENSG00000227857.1
2	lnc-TSPAN1-1	chr1:46600203-46600326	ENSG00000227857.2

Variant related genes	Relation type
PIK3R3	TF binding region
ENSG00000085998	Chromatin interaction
ENSG00000117461	Chromatin interaction
ENSG00000117472	Chromatin interaction
ENSG00000085999	Chromatin interaction
ENSG00000250719	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs2275425	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41292274	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4420029	1.00[JPT][hapmap]
rs58888694	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7542465	1.00[CEU][hapmap]

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	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
2	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
3	nsv871928	chr1:46024701-46609736	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
4	nsv1003517	chr1:46244432-46609881	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
6	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
7	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
8	esv2754420	chr1:46461580-46635180	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
9	nsv1006747	chr1:46476089-46655484	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
10	nsv534947	chr1:46476089-46655484	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
11	nsv1012418	chr1:46544842-46619890	Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
12	nsv534948	chr1:46544842-46619890	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
13	nsv1006530	chr1:46544842-46655484	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
14	nsv534949	chr1:46544842-46655484	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46599200-46601000	Flanking Active TSS	GM12878-XiMat	blood
2	chr1:46599200-46601600	Flanking Active TSS	Hela-S3	cervix
3	chr1:46599200-46603200	Weak transcription	Ovary	ovary
4	chr1:46599400-46600400	Enhancers	Aorta	Aorta
5	chr1:46599400-46600400	Enhancers	Brain Inferior Temporal Lobe	brain
6	chr1:46599400-46600400	Enhancers	Gastric	stomach
7	chr1:46599400-46600600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr1:46599400-46600600	Enhancers	Colonic Mucosa	Colon
9	chr1:46599400-46600600	Weak transcription	Small Intestine	intestine
10	chr1:46599400-46600800	Enhancers	Brain Cingulate Gyrus	brain
11	chr1:46599400-46601000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr1:46599400-46601200	Flanking Active TSS	Fetal Heart	heart
13	chr1:46599400-46602200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:46599400-46603200	Weak transcription	Liver	Liver
15	chr1:46599600-46600400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:46599600-46600400	Enhancers	Right Atrium	heart
17	chr1:46599600-46600600	Weak transcription	Colon Smooth Muscle	Colon
18	chr1:46599600-46600600	Enhancers	HSMM	muscle
19	chr1:46599600-46601000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:46599600-46601000	Enhancers	Adipose Nuclei	Adipose
21	chr1:46599600-46601000	Enhancers	Fetal Thymus	thymus
22	chr1:46599600-46601000	Enhancers	Psoas Muscle	Psoas
23	chr1:46599600-46601000	Enhancers	A549	lung
24	chr1:46599600-46601200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:46599600-46601200	Enhancers	Pancreatic Islets	Pancreatic Islet
26	chr1:46599600-46601200	Enhancers	Fetal Stomach	stomach
27	chr1:46599600-46601400	Enhancers	Muscle Satellite Cultured Cells	--
28	chr1:46599600-46601400	Weak transcription	Fetal Muscle Trunk	muscle
29	chr1:46599600-46601600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr1:46599600-46601600	Enhancers	Fetal Muscle Leg	muscle
31	chr1:46599600-46601600	Enhancers	Left Ventricle	heart
32	chr1:46599600-46603200	Weak transcription	HSMMtube	muscle
33	chr1:46599600-46604000	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr1:46599800-46600400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:46599800-46600600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
36	chr1:46599800-46600600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr1:46599800-46600600	Enhancers	Stomach Smooth Muscle	stomach
38	chr1:46599800-46600800	Weak transcription	Brain Angular Gyrus	brain
39	chr1:46599800-46601000	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr1:46599800-46601000	Enhancers	K562	blood
41	chr1:46599800-46601000	Enhancers	NH-A	brain
42	chr1:46599800-46601000	Enhancers	NHLF	lung
43	chr1:46599800-46601200	Enhancers	HMEC	breast
44	chr1:46599800-46601600	Enhancers	Skeletal Muscle Male	skeletal muscle
45	chr1:46599800-46603200	Weak transcription	Duodenum Mucosa	Duodenum
46	chr1:46600000-46600400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:46600000-46600400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr1:46600000-46600400	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr1:46600000-46600600	Enhancers	Dnd41	blood
50	chr1:46600000-46600800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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