Variant report

Variant	rs12815116
Chromosome Location	chr12:75901300-75901301
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:75872783..75874994-chr12:75900196..75902850,2	K562	blood:

Variant related genes	Relation type
ENSG00000139278	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11180552	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11180560	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11355	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11540407	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11609405	0.80[ASN][1000 genomes]
rs11610328	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11611121	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11611609	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11612665	0.83[ASN][1000 genomes]
rs12425122	0.84[ASN][1000 genomes]
rs12811160	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12812559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12819511	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12822366	0.83[ASN][1000 genomes]
rs12822493	0.81[ASN][1000 genomes]
rs12822505	0.83[ASN][1000 genomes]
rs12826635	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12827668	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12827986	0.81[ASN][1000 genomes]
rs1501634	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs15513	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1552039	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1604381	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17217158	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17218895	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17818307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1824981	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2054517	0.81[ASN][1000 genomes]
rs2070162	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2202105	0.83[ASN][1000 genomes]
rs2279244	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306391	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34508642	0.83[ASN][1000 genomes]
rs35124104	0.84[ASN][1000 genomes]
rs35244242	0.83[ASN][1000 genomes]
rs35351465	0.83[ASN][1000 genomes]
rs35619460	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3741495	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3809118	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3809121	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4420306	0.83[ASN][1000 genomes]
rs4760596	0.83[ASN][1000 genomes]
rs56049502	0.81[ASN][1000 genomes]
rs61933361	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61933362	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61933387	0.81[ASN][1000 genomes]
rs7961005	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
7	nsv470305	chr12:75896688-75987360	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	esv3489219	chr12:75900625-75902132	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
9	esv3489230	chr12:75900683-75902058	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
10	esv3489241	chr12:75900683-75902058	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12815116	KRR1	cis	Muscle Skeletal	GTEx
rs12815116	GLIPR1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:75875600-75903400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr12:75875800-75903000	Weak transcription	Small Intestine	intestine
3	chr12:75875800-75903600	Weak transcription	Fetal Intestine Small	intestine
4	chr12:75876200-75903400	Weak transcription	Fetal Stomach	stomach
5	chr12:75879800-75902000	Strong transcription	Primary B cells from cord blood	blood
6	chr12:75880600-75903800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr12:75882600-75903200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr12:75883200-75901800	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr12:75883400-75902600	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr12:75883600-75901800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr12:75883600-75902200	Strong transcription	Primary B cells from peripheral blood	blood
12	chr12:75883800-75904800	Weak transcription	Esophagus	oesophagus
13	chr12:75884200-75902200	Strong transcription	Primary T helper cells PMA-I stimulated	--
14	chr12:75884400-75901600	Strong transcription	NHDF-Ad	bronchial
15	chr12:75885000-75902200	Strong transcription	HUVEC	blood vessel
16	chr12:75885000-75902400	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr12:75886200-75903200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr12:75886600-75901400	Strong transcription	HMEC	breast
19	chr12:75886600-75903000	Strong transcription	Fetal Thymus	thymus
20	chr12:75886800-75902000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr12:75887000-75902200	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr12:75887200-75902200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr12:75887400-75901800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr12:75887400-75903000	Strong transcription	HUES6 Cell Line	embryonic stem cell
25	chr12:75887600-75901800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr12:75887600-75902000	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr12:75887600-75902000	Strong transcription	Duodenum Mucosa	Duodenum
28	chr12:75887600-75902400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr12:75887800-75902600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr12:75888000-75903000	Weak transcription	Pancreas	Pancrea
31	chr12:75888600-75901800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr12:75888600-75903200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr12:75888800-75902200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr12:75888800-75903800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr12:75888800-75904200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr12:75889000-75901600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr12:75889000-75901800	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr12:75889000-75901800	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr12:75889200-75901400	Strong transcription	Stomach Smooth Muscle	stomach
40	chr12:75890200-75901800	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr12:75890200-75902000	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr12:75890600-75901800	Strong transcription	NHEK	skin
43	chr12:75890600-75903200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr12:75891400-75903800	Weak transcription	Fetal Brain Male	brain
45	chr12:75892400-75902400	Strong transcription	K562	blood
46	chr12:75892800-75904400	Weak transcription	Gastric	stomach
47	chr12:75893800-75903600	Weak transcription	Stomach Mucosa	stomach
48	chr12:75895400-75903000	Weak transcription	Ovary	ovary
49	chr12:75895400-75903800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr12:75895400-75903800	Weak transcription	Brain Substantia Nigra	brain

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