Variant report

Variant	rs10879921
Chromosome Location	chr12:75878563-75878564
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:75871827..75875273-chr12:75876446..75879780,3	K562	blood:
2	chr12:75877168..75879859-chr12:75887104..75889519,2	K562	blood:
3	chr12:75873773..75875843-chr12:75876360..75879179,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KRR1-1	chr12:75877904-75878670	ENSG00000257497.1

Variant related genes	Relation type
ENSG00000139278	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10785191	0.89[ASN][1000 genomes]
rs10879914	0.89[ASN][1000 genomes]
rs11180516	0.88[ASN][1000 genomes]
rs11180517	0.88[ASN][1000 genomes]
rs11180523	0.89[ASN][1000 genomes]
rs11180529	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs11180553	0.91[EUR][1000 genomes]
rs12305941	0.90[ASN][1000 genomes]
rs2102134	0.88[ASN][1000 genomes]
rs2279245	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34217466	0.82[ASN][1000 genomes]
rs4882599	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492067	chr12:75415458-76077537	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1036987	chr12:75415532-76101559	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv899313	chr12:75715330-76057811	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	nsv1040583	chr12:75742802-76360276	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv428592	chr12:75766619-75936721	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv948653	chr12:75773464-76220618	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10879921	GLIPR1L2	cis	Artery Tibial	GTEx

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75873400-75878800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr12:75873800-75879000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr12:75874800-75895000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr12:75875400-75887800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:75875600-75880600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr12:75875600-75882400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr12:75875600-75890200	Weak transcription	Brain Substantia Nigra	brain
8	chr12:75875600-75903400	Weak transcription	Brain Cingulate Gyrus	brain
9	chr12:75875800-75882800	Weak transcription	NHEK	skin
10	chr12:75875800-75883600	Weak transcription	Esophagus	oesophagus
11	chr12:75875800-75886600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:75875800-75886800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr12:75875800-75888800	Weak transcription	Fetal Muscle Trunk	muscle
14	chr12:75875800-75892400	Weak transcription	K562	blood
15	chr12:75875800-75892600	Weak transcription	Brain Angular Gyrus	brain
16	chr12:75875800-75894400	Weak transcription	Colonic Mucosa	Colon
17	chr12:75875800-75903000	Weak transcription	Small Intestine	intestine
18	chr12:75875800-75903600	Weak transcription	Fetal Intestine Small	intestine
19	chr12:75876000-75880600	Transcr. at gene 5' and 3'	Osteobl	bone
20	chr12:75876200-75878800	Weak transcription	A549	lung
21	chr12:75876200-75885000	Weak transcription	Liver	Liver
22	chr12:75876200-75903400	Weak transcription	Fetal Stomach	stomach
23	chr12:75876400-75878800	Active TSS	GM12878-XiMat	blood
24	chr12:75876400-75879200	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
25	chr12:75876400-75881200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr12:75876400-75883600	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr12:75876400-75886800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr12:75876400-75889800	Weak transcription	Lung	lung
29	chr12:75876400-75891400	Weak transcription	Fetal Muscle Leg	muscle
30	chr12:75876400-75894400	Weak transcription	Ovary	ovary
31	chr12:75876600-75879000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
32	chr12:75876600-75883200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr12:75876800-75879200	Transcr. at gene 5' and 3'	NH-A	brain
34	chr12:75876800-75889800	Weak transcription	Left Ventricle	heart
35	chr12:75876800-75889800	Weak transcription	Thymus	Thymus
36	chr12:75876800-75890400	Weak transcription	Brain Hippocampus Middle	brain
37	chr12:75876800-75895000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr12:75877000-75878600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr12:75877000-75879000	Enhancers	Primary T cells from cord blood	blood
40	chr12:75877200-75879000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr12:75877200-75879200	Genic enhancers	Primary neutrophils fromperipheralblood	blood
42	chr12:75877200-75880000	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr12:75877400-75878800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr12:75877400-75879000	Enhancers	H1 Cell Line	embryonic stem cell
45	chr12:75877400-75879200	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr12:75877400-75879200	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
47	chr12:75877400-75880400	Genic enhancers	Primary B cells from peripheral blood	blood
48	chr12:75877400-75880600	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
49	chr12:75877600-75878600	Genic enhancers	Primary T cells fromperipheralblood	blood
50	chr12:75877600-75878800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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