Variant report

Variant	rs2070162
Chromosome Location	chr12:75900588-75900589
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	POLR2A	chr12:75898028-75900893	U87	brain:	n/a	n/a
2	POLR2A	chr12:75900386-75900740	GM12892	blood:	n/a	n/a
3	POLR2A	chr12:75900405-75900594	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr12:75900331-75900840	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:75899037..75901199-chr12:75907955..75910406,2	K562	blood:
2	chr12:75872783..75874994-chr12:75900196..75902850,2	K562	blood:

Variant related genes	Relation type
KRR1	TF binding region
ENSG00000139278	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10506667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11180480	0.81[JPT][hapmap]
rs11180552	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11180560	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];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]
rs1147995	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11540407	0.92[ASW][hapmap];0.94[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];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	0.83[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11611121	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11611609	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];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[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12815116	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12819511	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12822366	0.83[ASN][1000 genomes]
rs12822493	1.00[CHB][hapmap];0.82[JPT][hapmap];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	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs15513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1552039	0.84[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];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	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2202105	0.83[ASN][1000 genomes]
rs2279244	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];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[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3809118	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];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:7 , 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

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs2070162	GLIPR1L2	cis	parietal	SCAN
rs2070162	GLIPR1L2	cis	cerebellum	SCAN
rs2070162	GLIPR1	cis	lymphoblastoid	seeQTL
rs2070162	PTPRB	cis	parietal	SCAN
rs2070162	KRR1	cis	parietal	SCAN
rs2070162	GLIPR1	cis	uninvolved skin	skin_eQTL
rs2070162	KRR1	cis	cerebellum	SCAN
rs2070162	LRRN1	trans	cerebellum	SCAN
rs2070162	GLIPR1	cis	lesional skin	skin_eQTL
rs2070162	GLIPR1	cis	normal skin	skin_eQTL
rs2070162	GLIPR1	cis	parietal	SCAN
rs2070162	KRR1	cis	Muscle Skeletal	GTEx

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	chr12:75879200-75900600	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr12:75879800-75902000	Strong transcription	Primary B cells from cord blood	blood
7	chr12:75880600-75903800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr12:75882600-75903200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr12:75883200-75901800	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr12:75883400-75902600	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr12:75883600-75901800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr12:75883600-75902200	Strong transcription	Primary B cells from peripheral blood	blood
13	chr12:75883800-75904800	Weak transcription	Esophagus	oesophagus
14	chr12:75884200-75901200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr12:75884200-75901200	Strong transcription	NH-A	brain
16	chr12:75884200-75902200	Strong transcription	Primary T helper cells PMA-I stimulated	--
17	chr12:75884400-75901600	Strong transcription	NHDF-Ad	bronchial
18	chr12:75885000-75902200	Strong transcription	HUVEC	blood vessel
19	chr12:75885000-75902400	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr12:75886200-75903200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr12:75886600-75901400	Strong transcription	HMEC	breast
22	chr12:75886600-75903000	Strong transcription	Fetal Thymus	thymus
23	chr12:75886800-75902000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr12:75887000-75900600	Strong transcription	A549	lung
25	chr12:75887000-75902200	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr12:75887200-75901000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr12:75887200-75902200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr12:75887400-75901800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr12:75887400-75903000	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr12:75887600-75901200	Strong transcription	Dnd41	blood
31	chr12:75887600-75901800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr12:75887600-75902000	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr12:75887600-75902000	Strong transcription	Duodenum Mucosa	Duodenum
34	chr12:75887600-75902400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr12:75887800-75902600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:75888000-75903000	Weak transcription	Pancreas	Pancrea
37	chr12:75888600-75900800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr12:75888600-75901800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr12:75888600-75903200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr12:75888800-75902200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr12:75888800-75903800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr12:75888800-75904200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr12:75889000-75900600	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr12:75889000-75901000	Strong transcription	Adipose Nuclei	Adipose
45	chr12:75889000-75901600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr12:75889000-75901800	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr12:75889000-75901800	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr12:75889200-75901400	Strong transcription	Stomach Smooth Muscle	stomach
49	chr12:75890200-75900600	Strong transcription	Fetal Intestine Large	intestine
50	chr12:75890200-75901800	Strong transcription	Duodenum Smooth Muscle	Duodenum

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