Variant report

Variant	rs2157580
Chromosome Location	chr1:169457596-169457597
allele	G/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	CEBPB	chr1:169457319-169457652	K562	blood:	n/a	chr1:169457482-169457493
2	RCOR1	chr1:169457358-169457758	K562	blood:	n/a	n/a
3	SPI1	chr1:169457494-169457738	K562	blood:	n/a	n/a
4	SPI1	chr1:169457460-169457727	K562	blood:	n/a	n/a
5	SPI1	chr1:169457393-169457805	HL-60	blood:	n/a	n/a
6	KAP1	chr1:169455068-169457749	HEK293	kidney:	n/a	chr1:169456899-169456907 chr1:169456870-169456878
7	CEBPB	chr1:169457317-169457605	HepG2	liver:	n/a	chr1:169457482-169457493
8	HDAC2	chr1:169457405-169457753	K562	blood:	n/a	n/a
9	SPI1	chr1:169457452-169457807	HL-60	blood:	n/a	n/a
10	TEAD4	chr1:169457359-169457771	K562	blood:	n/a	n/a
11	RCOR1	chr1:169457231-169457771	K562	blood:	n/a	n/a
12	GABPA	chr1:169457425-169457719	K562	blood:	n/a	n/a
13	CEBPB	chr1:169457330-169457627	A549	lung:	n/a	chr1:169457482-169457493
14	TAL1	chr1:169457430-169457670	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:169449894..169459462-chr1:169475885..169501963,75	MCF-7	breast:
2	chr1:169456428..169460568-chr1:169464667..169468195,6	K562	blood:
3	chr1:169454326..169457851-chr1:169761976..169765744,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BLZF1-2	chr1:169455353-169458414	NONHSAT007465

Variant related genes	Relation type
SLC19A2	TF binding region
ENSG00000198734	Chromatin interaction
ENSG00000171806	Chromatin interaction
ENSG00000000460	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12408451	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2056926	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv831871	chr1:169320673-169486680	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1001454	chr1:169387381-169465274	Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2157580	NME7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169454400-169458400	Active TSS	Skeletal Muscle Male	skeletal muscle
2	chr1:169455800-169457600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:169455800-169457800	Enhancers	Sigmoid Colon	Sigmoid Colon
4	chr1:169455800-169461400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:169456000-169457600	Flanking Active TSS	Liver	Liver
6	chr1:169456000-169460400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr1:169456200-169457800	Enhancers	Fetal Muscle Leg	muscle
8	chr1:169456200-169457800	Enhancers	Small Intestine	intestine
9	chr1:169456200-169464000	Weak transcription	Esophagus	oesophagus
10	chr1:169456400-169457600	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr1:169456400-169457800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr1:169456400-169458000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr1:169456400-169461000	Weak transcription	Fetal Lung	lung
14	chr1:169456600-169457600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr1:169456600-169457600	Weak transcription	Dnd41	blood
16	chr1:169456600-169461000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:169456600-169461000	Weak transcription	NHDF-Ad	bronchial
18	chr1:169456600-169462200	Weak transcription	Placenta	Placenta
19	chr1:169456600-169464200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:169456600-169464200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:169456600-169464200	Weak transcription	HMEC	breast
22	chr1:169456800-169457600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr1:169456800-169457800	Enhancers	Hela-S3	cervix
24	chr1:169456800-169457800	Enhancers	K562	blood
25	chr1:169456800-169458400	Enhancers	Fetal Heart	heart
26	chr1:169456800-169460800	Weak transcription	Osteobl	bone
27	chr1:169456800-169461200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr1:169457000-169457600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
29	chr1:169457000-169457800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr1:169457000-169457800	Enhancers	Left Ventricle	heart
31	chr1:169457000-169457800	Enhancers	Pancreas	Pancrea
32	chr1:169457000-169458800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr1:169457000-169459000	Enhancers	HepG2	liver
34	chr1:169457000-169460400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:169457000-169460400	Weak transcription	GM12878-XiMat	blood
36	chr1:169457000-169461000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:169457000-169463800	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr1:169457000-169464400	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr1:169457200-169457600	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr1:169457200-169457800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
41	chr1:169457200-169457800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:169457200-169458000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr1:169457200-169458000	Flanking Active TSS	Psoas Muscle	Psoas
44	chr1:169457200-169458600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr1:169457400-169457600	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr1:169457400-169457600	Enhancers	Muscle Satellite Cultured Cells	--
47	chr1:169457400-169457600	Enhancers	HSMM	muscle
48	chr1:169457400-169458200	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr1:169457400-169461000	Weak transcription	HSMMtube	muscle

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