Variant report

Variant	rs17619893
Chromosome Location	chr12:21590003-21590004
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	MAFF	chr12:21589912-21590185	K562	blood:	n/a	n/a
2	MAFK	chr12:21589952-21590142	HepG2	liver:	n/a	n/a
3	BHLHE40	chr12:21589970-21591037	GM12878	blood:	n/a	n/a
4	MAFF	chr12:21589929-21590190	HepG2	liver:	n/a	n/a
5	CHD2	chr12:21589990-21591047	GM12878	blood:	n/a	n/a
6	POLR2A	chr12:21589992-21592247	MCF10A-Er-Src	breast:	n/a	n/a
7	MAFK	chr12:21589939-21590165	HepG2	liver:	n/a	n/a
8	PML	chr12:21589968-21591240	GM12878	blood:	n/a	chr12:21590929-21590937
9	MXI1	chr12:21589869-21591503	IMR90	lung:	n/a	n/a
10	HCFC1	chr12:21588964-21591600	Hela-S3	cervix:	n/a	n/a
11	MYC	chr12:21589957-21591389	NB4	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:21569338..21572113-chr12:21589171..21592854,4	K562	blood:
2	chr12:21569338..21572113-chr12:21589171..21592483,4	K562	blood:
3	chr12:21589456..21592020-chr12:21808889..21812230,4	K562	blood:

Variant related genes	Relation type
PYROXD1	TF binding region
ENSG00000111716	Chromatin interaction
ENSG00000084453	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs17683246	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34462155	1.00[AFR][1000 genomes]
rs45628437	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526789	chr12:21555691-21590788	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
2	nsv898895	chr12:21561645-21621891	Weak transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
3	nsv898896	chr12:21561645-21695584	Strong transcription Bivalent Enhancer Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1043936	chr12:21562673-21979030	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
5	nsv557741	chr12:21578559-22169854	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv469163	chr12:21579080-21592357	Active TSS Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases
7	nsv557742	chr12:21579080-21592357	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17619893	GOLT1B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21587200-21590200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:21589400-21590200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr12:21589800-21590200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr12:21589800-21590200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr12:21589800-21590200	Flanking Active TSS	Hela-S3	cervix
6	chr12:21589800-21590200	Flanking Active TSS	HMEC	breast
7	chr12:21589800-21590200	Flanking Active TSS	K562	blood
8	chr12:21589800-21590200	Flanking Active TSS	Osteobl	bone
9	chr12:21589800-21590400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr12:21589800-21591400	Active TSS	Fetal Kidney	kidney
11	chr12:21589800-21591600	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr12:21589800-21591600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr12:21589800-21591600	Active TSS	Breast Myoepithelial Primary Cells	Breast
14	chr12:21589800-21591600	Active TSS	HSMMtube	muscle
15	chr12:21589800-21592000	Active TSS	Rectal Mucosa Donor 29	rectum
16	chr12:21590000-21590200	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr12:21590000-21590200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
18	chr12:21590000-21590200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr12:21590000-21590200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr12:21590000-21590200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr12:21590000-21590200	Active TSS	Primary B cells from cord blood	blood
22	chr12:21590000-21590200	Enhancers	Primary B cells from peripheral blood	blood
23	chr12:21590000-21590200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
24	chr12:21590000-21590200	Enhancers	Primary hematopoietic stem cells	blood
25	chr12:21590000-21590200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
26	chr12:21590000-21590200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr12:21590000-21590200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
28	chr12:21590000-21590200	Flanking Active TSS	Brain Germinal Matrix	brain
29	chr12:21590000-21590200	Flanking Active TSS	Brain Substantia Nigra	brain
30	chr12:21590000-21590200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
31	chr12:21590000-21590200	Enhancers	Fetal Lung	lung
32	chr12:21590000-21590200	Flanking Active TSS	Fetal Muscle Leg	muscle
33	chr12:21590000-21590200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
34	chr12:21590000-21590200	Flanking Bivalent TSS/Enh	Thymus	Thymus
35	chr12:21590000-21590200	Flanking Active TSS	A549	lung
36	chr12:21590000-21590200	Flanking Active TSS	HepG2	liver
37	chr12:21590000-21590400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
38	chr12:21590000-21590400	Flanking Active TSS	Primary T cells from cord blood	blood
39	chr12:21590000-21590400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
40	chr12:21590000-21590400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
41	chr12:21590000-21590400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
42	chr12:21590000-21590400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
43	chr12:21590000-21590400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
44	chr12:21590000-21590400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr12:21590000-21590400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr12:21590000-21590400	Flanking Active TSS	Brain Cingulate Gyrus	brain
47	chr12:21590000-21590400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
48	chr12:21590000-21590400	Flanking Active TSS	Duodenum Mucosa	Duodenum
49	chr12:21590000-21590400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
50	chr12:21590000-21590400	Enhancers	Small Intestine	intestine

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