Variant report

Variant	rs12138875
Chromosome Location	chr1:169457028-169457029
allele	A/G
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	KAP1	chr1:169455068-169457749	HEK293	kidney:	n/a	chr1:169456899-169456907 chr1:169456870-169456878
2	POLR2A	chr1:169456976-169457205	HepG2	liver:	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
ENSG00000171806	Chromatin interaction
ENSG00000000460	Chromatin interaction
ENSG00000198734	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs6427193	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6656463	0.80[AMR][1000 genomes]
rs6695137	0.80[AMR][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
rs12138875	NME7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169453600-169457200	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr1:169454400-169458400	Active TSS	Skeletal Muscle Male	skeletal muscle
3	chr1:169455600-169457400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
4	chr1:169455800-169457200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:169455800-169457200	Flanking Active TSS	HSMMtube	muscle
6	chr1:169455800-169457600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:169455800-169457800	Enhancers	Sigmoid Colon	Sigmoid Colon
8	chr1:169455800-169461400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:169456000-169457600	Flanking Active TSS	Liver	Liver
10	chr1:169456000-169460400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr1:169456200-169457200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:169456200-169457200	Enhancers	Fetal Brain Male	brain
13	chr1:169456200-169457800	Enhancers	Fetal Muscle Leg	muscle
14	chr1:169456200-169457800	Enhancers	Small Intestine	intestine
15	chr1:169456200-169464000	Weak transcription	Esophagus	oesophagus
16	chr1:169456400-169457200	Enhancers	H1 Cell Line	embryonic stem cell
17	chr1:169456400-169457200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:169456400-169457200	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr1:169456400-169457200	Enhancers	Brain Anterior Caudate	brain
20	chr1:169456400-169457200	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr1:169456400-169457200	Active TSS	Psoas Muscle	Psoas
22	chr1:169456400-169457200	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr1:169456400-169457600	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr1:169456400-169457800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr1:169456400-169458000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr1:169456400-169461000	Weak transcription	Fetal Lung	lung
27	chr1:169456600-169457600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr1:169456600-169457600	Weak transcription	Dnd41	blood
29	chr1:169456600-169461000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr1:169456600-169461000	Weak transcription	NHDF-Ad	bronchial
31	chr1:169456600-169462200	Weak transcription	Placenta	Placenta
32	chr1:169456600-169464200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:169456600-169464200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:169456600-169464200	Weak transcription	HMEC	breast
35	chr1:169456800-169457200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr1:169456800-169457200	Active TSS	Pancreatic Islets	Pancreatic Islet
37	chr1:169456800-169457200	Enhancers	Fetal Muscle Trunk	muscle
38	chr1:169456800-169457200	Active TSS	HSMM	muscle
39	chr1:169456800-169457600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
40	chr1:169456800-169457800	Enhancers	Hela-S3	cervix
41	chr1:169456800-169457800	Enhancers	K562	blood
42	chr1:169456800-169458400	Enhancers	Fetal Heart	heart
43	chr1:169456800-169460800	Weak transcription	Osteobl	bone
44	chr1:169456800-169461200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr1:169457000-169457200	Active TSS	ES-I3 Cell Line	embryonic stem cell
46	chr1:169457000-169457200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr1:169457000-169457200	Enhancers	Aorta	Aorta
48	chr1:169457000-169457200	Enhancers	Right Atrium	heart
49	chr1:169457000-169457200	Enhancers	Right Ventricle	heart
50	chr1:169457000-169457400	Enhancers	iPS-18 Cell Line	embryonic stem cell

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