Variant report

Variant	rs587555
Chromosome Location	chr3:101571550-101571551
allele	C/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	POLR2A	chr3:101567198-101574916	GM12878	blood:	n/a	n/a
2	SPI1	chr3:101571201-101571627	GM12878	blood:	n/a	chr3:101571533-101571540 chr3:101571530-101571543 chr3:101571405-101571418 chr3:101571532-101571541 chr3:101571407-101571416 chr3:101571404-101571417
3	POLR2A	chr3:101565720-101574900	GM12891	blood:	n/a	n/a
4	POLR2A	chr3:101567627-101574860	GM12878	blood:	n/a	n/a
5	SPI1	chr3:101571201-101571555	GM12891	blood:	n/a	chr3:101571533-101571540 chr3:101571530-101571543 chr3:101571405-101571418 chr3:101571532-101571541 chr3:101571407-101571416 chr3:101571404-101571417
6	POLR2A	chr3:101571512-101574724	GM18505	blood:	n/a	n/a
7	POLR2A	chr3:101567742-101571937	Hela-S3	cervix:	n/a	n/a
8	SPI1	chr3:101571146-101571556	GM12891	blood:	n/a	chr3:101571533-101571540 chr3:101571530-101571543 chr3:101571405-101571418 chr3:101571532-101571541 chr3:101571407-101571416 chr3:101571404-101571417
9	POLR2A	chr3:101569085-101574846	HepG2	liver:	n/a	n/a
10	POLR2A	chr3:101567553-101574820	IMR90	lung:	n/a	n/a
11	POLR2A	chr3:101567615-101574974	SK-N-SH	brain:	n/a	n/a
12	CHD1	chr3:101568171-101574913	IMR90	lung:	n/a	n/a
13	CUX1	chr3:101570565-101571652	GM12878	blood:	n/a	n/a
14	SPI1	chr3:101571077-101571772	GM12878	blood:	n/a	chr3:101571533-101571540 chr3:101571530-101571543 chr3:101571405-101571418 chr3:101571532-101571541 chr3:101571407-101571416 chr3:101571404-101571417
15	POLR2A	chr3:101567371-101573695	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr3:101567162-101574755	MCF10A-Er-Src	breast:	n/a	n/a
17	POLR2A	chr3:101568040-101574948	GM12878	blood:	n/a	n/a
18	POLR2A	chr3:101567611-101574981	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:101569866..101571577-chr3:101831085..101832686,2	MCF-7	breast:
2	chr3:101569504..101571608-chr3:101590460..101592111,2	K562	blood:
3	chr3:101570369..101573097-chr3:101618307..101620488,2	MCF-7	breast:
4	chr3:101570653..101572581-chr3:101834982..101836970,2	MCF-7	breast:
5	chr3:101544475..101550800-chr3:101565965..101572617,10	K562	blood:
6	chr3:101543661..101554550-chr3:101566310..101574179,30	MCF-7	breast:
7	chr3:101544575..101547702-chr3:101571117..101572871,3	K562	blood:
8	chr3:101570052..101571665-chr3:101611707..101614656,2	MCF-7	breast:
9	chr3:101570471..101572407-chr3:101832764..101834388,2	MCF-7	breast:

Variant related genes	Relation type
NFKBIZ	TF binding region
ENSG00000144802	Chromatin interaction
ENSG00000249474	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs14134	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2925332	0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2925333	0.80[ASN][1000 genomes]
rs2926539	0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2926540	0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs592332	0.88[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs592779	0.91[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs599849	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs601225	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs618901	0.81[ASN][1000 genomes]
rs622122	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs654219	0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs665374	0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs677011	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs678354	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs680508	0.93[ASN][1000 genomes]
rs681573	0.91[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs688058	0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs694293	0.85[AFR][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	nsv497784	chr3:101315009-102092989	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv997407	chr3:101384031-101611391	Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv536675	chr3:101384031-101611391	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	esv3351469	chr3:101511702-101866448	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101568600-101572600	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
2	chr3:101568800-101572400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
3	chr3:101569200-101573600	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr3:101569400-101573000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr3:101569800-101571800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:101569800-101572000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:101569800-101576400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:101570000-101572000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:101570000-101572600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr3:101570000-101572600	Transcr. at gene 5' and 3'	HSMM	muscle
11	chr3:101570000-101574400	Weak transcription	Fetal Brain Female	brain
12	chr3:101570000-101578000	Weak transcription	Brain Germinal Matrix	brain
13	chr3:101570000-101579200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:101570200-101571600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:101570200-101571600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:101570200-101574800	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
17	chr3:101570400-101571600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:101570400-101571600	Weak transcription	Fetal Kidney	kidney
19	chr3:101570400-101571800	Weak transcription	Brain Angular Gyrus	brain
20	chr3:101570400-101573000	Transcr. at gene 5' and 3'	Primary monocytes fromperipheralblood	blood
21	chr3:101570400-101574800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
22	chr3:101570400-101598400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr3:101570600-101571800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr3:101570600-101572000	Transcr. at gene 5' and 3'	Primary T helper cells fromperipheralblood	blood
25	chr3:101570600-101572200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr3:101570600-101572600	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:101570600-101572600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells	blood
28	chr3:101570600-101572600	Transcr. at gene 5' and 3'	Liver	Liver
29	chr3:101570600-101572600	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
30	chr3:101570600-101573200	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
31	chr3:101570600-101573200	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
32	chr3:101570600-101574200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
33	chr3:101570600-101577600	Transcr. at gene 5' and 3'	Fetal Intestine Large	intestine
34	chr3:101570800-101571600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:101570800-101571600	Transcr. at gene 5' and 3'	HUVEC	blood vessel
36	chr3:101570800-101571800	Weak transcription	Fetal Brain Male	brain
37	chr3:101570800-101572400	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 31	rectum
38	chr3:101570800-101572800	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:101570800-101576600	Transcr. at gene 5' and 3'	Duodenum Mucosa	Duodenum
40	chr3:101570800-101579400	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr3:101570800-101580600	Strong transcription	H1 Cell Line	embryonic stem cell
42	chr3:101570800-101580600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr3:101570800-101580800	Strong transcription	HUES6 Cell Line	embryonic stem cell
44	chr3:101570800-101580800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
45	chr3:101571000-101571600	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
46	chr3:101571000-101571600	Weak transcription	Thymus	Thymus
47	chr3:101571000-101571800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr3:101571000-101572000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr3:101571000-101572400	Transcr. at gene 5' and 3'	Adipose Nuclei	Adipose
50	chr3:101571000-101574200	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum

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