Variant report

Variant	rs2999158
Chromosome Location	chr1:113239478-113239479
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:16 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:113239443-113239697	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr1:113239414-113239633	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:113239363-113239782	K562	blood:	n/a	n/a
4	POLR2A	chr1:113237535-113239993	A549	lung:	n/a	n/a
5	POLR2A	chr1:113238764-113239774	HepG2	liver:	n/a	n/a
6	POLR2A	chr1:113238690-113239853	K562	blood:	n/a	n/a
7	GATA1	chr1:113239474-113239986	PBDE	blood:	n/a	chr1:113239681-113239690 chr1:113239676-113239683
8	TEAD4	chr1:113239356-113239952	K562	blood:	n/a	n/a
9	POLR2A	chr1:113239477-113239640	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr1:113238492-113239893	K562	blood:	n/a	n/a
11	POLR2A	chr1:113238749-113239579	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr1:113239157-113239686	K562	blood:	n/a	n/a
13	POLR2A	chr1:113238769-113239679	GM12892	blood:	n/a	n/a
14	POLR2A	chr1:113239400-113239490	HepG2	liver:	n/a	n/a
15	POLR2A	chr1:113238763-113239628	HepG2	liver:	n/a	n/a
16	POLR2A	chr1:113239325-113239493	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:113159779..113171222-chr1:113238237..113251191,41	K562	blood:
2	chr1:113214866..113222565-chr1:113237012..113253952,54	K562	blood:
3	chr1:113160176..113163931-chr1:113238020..113242018,6	K562	blood:
4	chr1:113215224..113219998-chr1:113238829..113244717,20	MCF-7	breast:
5	chr1:113214002..113222947-chr1:113236890..113251579,47	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000225075	TF binding region
MOV10	TF binding region
ENSG00000116489	Chromatin interaction
ENSG00000235299	Chromatin interaction
ENSG00000155363	Chromatin interaction
ENSG00000007341	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs2279500	0.81[AFR][1000 genomes]
rs2999159	0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv13370	chr1:112693290-113246263	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
4	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
5	nsv533295	chr1:113167645-113589588	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
6	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
8	nsv529238	chr1:113229946-113759080	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
9	esv997362	chr1:113234820-113243297	Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2999158	ST7L	cis	multi-tissue	Pritchard
rs2999158	ST7L	Cis_1M	lymphoblastoid	RTeQTL
rs2999158	ST7L	cis	Thyroid	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113218600-113240800	Weak transcription	Right Atrium	heart
2	chr1:113219000-113242200	Weak transcription	NHDF-Ad	bronchial
3	chr1:113219000-113243800	Weak transcription	Fetal Brain Male	brain
4	chr1:113222000-113243000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:113228600-113242800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:113228600-113242800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr1:113229000-113242200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr1:113229200-113248000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr1:113229600-113243200	Strong transcription	Dnd41	blood
10	chr1:113230200-113239800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr1:113230200-113240200	Weak transcription	Fetal Heart	heart
12	chr1:113230200-113240600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:113230200-113240800	Strong transcription	Adipose Nuclei	Adipose
14	chr1:113230200-113241200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:113230200-113242600	Strong transcription	Primary T helper cells fromperipheralblood	blood
16	chr1:113230200-113243000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:113230200-113243200	Strong transcription	Primary T cells from cord blood	blood
18	chr1:113230400-113240400	Strong transcription	HepG2	liver
19	chr1:113230400-113240600	Strong transcription	Stomach Smooth Muscle	stomach
20	chr1:113230400-113241200	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr1:113230600-113240800	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr1:113230600-113241000	Strong transcription	Gastric	stomach
23	chr1:113230600-113241400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:113230600-113242000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr1:113230600-113242000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:113230600-113242200	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr1:113230600-113242600	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr1:113230800-113239800	Strong transcription	Liver	Liver
29	chr1:113230800-113240000	Strong transcription	Duodenum Mucosa	Duodenum
30	chr1:113230800-113241400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
31	chr1:113231200-113241400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr1:113231400-113241800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr1:113231600-113241200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:113231600-113243000	Weak transcription	Psoas Muscle	Psoas
35	chr1:113231600-113243200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr1:113231800-113239800	Strong transcription	HMEC	breast
37	chr1:113231800-113240000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr1:113231800-113240400	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr1:113231800-113242400	Strong transcription	Osteobl	bone
40	chr1:113231800-113242600	Strong transcription	Fetal Lung	lung
41	chr1:113232000-113240400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr1:113232000-113241000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
43	chr1:113232000-113241000	Strong transcription	Hela-S3	cervix
44	chr1:113232000-113241400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr1:113232000-113242400	Strong transcription	Fetal Stomach	stomach
46	chr1:113232000-113242600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr1:113232200-113240000	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr1:113232200-113240600	Strong transcription	Colonic Mucosa	Colon
49	chr1:113232200-113241000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr1:113232200-113241400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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