Variant report

Variant	rs12946619
Chromosome Location	chr17:16146659-16146660
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:16145216..16149469-chr17:16187670..16191741,4	K562	blood:

Extended variants
information (count: 68 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1029809	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs11650427	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs11652044	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11653500	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11653650	0.83[EUR][1000 genomes]
rs11655325	0.84[EUR][1000 genomes]
rs12150285	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12936233	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs12938394	0.85[EUR][1000 genomes]
rs12945855	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs12945959	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12948244	0.87[EUR][1000 genomes]
rs178785	0.85[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs178787	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs178788	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs178814	0.82[CEU][hapmap];0.92[CHB][hapmap]
rs178815	0.82[CEU][hapmap];0.84[CHB][hapmap];0.84[GIH][hapmap]
rs178822	0.82[CEU][hapmap];0.92[CHB][hapmap];0.84[GIH][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]
rs178838	0.81[CEU][hapmap];0.92[CHB][hapmap]
rs178839	0.82[CEU][hapmap]
rs2014604	0.85[GIH][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs2078050	0.82[ASW][hapmap];0.82[CEU][hapmap];0.92[CHB][hapmap];0.94[LWK][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap]
rs2157990	0.84[CHB][hapmap];0.81[TSI][hapmap]
rs2157991	0.82[CEU][hapmap];0.92[CHB][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]
rs2324141	0.82[CEU][hapmap];0.92[CHB][hapmap];0.82[CHD][hapmap];0.84[GIH][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]
rs2324142	0.82[ASW][hapmap];0.82[CEU][hapmap];0.92[CHB][hapmap];0.84[GIH][hapmap];0.91[LWK][hapmap];0.87[MEX][hapmap];0.87[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs28516015	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs3095171	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3112511	0.88[ASW][hapmap];0.85[GIH][hapmap];0.94[LWK][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs3112513	0.88[ASW][hapmap];0.85[GIH][hapmap];0.91[LWK][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs34331598	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35565381	0.88[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs3785621	0.83[GIH][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs3785623	0.83[GIH][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs3785628	0.82[ASW][hapmap];0.82[CEU][hapmap];0.92[CHB][hapmap];0.94[LWK][hapmap];0.87[MEX][hapmap];0.86[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap]
rs4435297	0.92[CHB][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs4470185	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4791665	0.85[GIH][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs4792717	0.82[CEU][hapmap];0.92[CHB][hapmap]
rs4792718	0.91[MEX][hapmap]
rs4792730	0.86[EUR][1000 genomes]
rs56269147	0.88[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs62072527	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62072528	0.83[EUR][1000 genomes]
rs6502499	0.80[EUR][1000 genomes]
rs7210990	0.84[CEU][hapmap]
rs7214695	0.82[CEU][hapmap];0.92[CHB][hapmap];1.00[YRI][hapmap]
rs7215071	0.82[EUR][1000 genomes]
rs7219687	0.85[GIH][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs7223346	0.82[CEU][hapmap];0.92[CHB][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]
rs7223428	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7225920	0.86[EUR][1000 genomes]
rs8073259	1.00[ASW][hapmap];0.88[CEU][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8079969	0.82[CEU][hapmap];0.92[CHB][hapmap];0.84[GIH][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]
rs9747114	0.84[EUR][1000 genomes]
rs9890539	0.82[TSI][hapmap]
rs9909022	0.81[EUR][1000 genomes]
rs9910148	0.85[CEU][hapmap]
rs9916220	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934185	chr17:15552960-16551197	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	190 gene(s)	inside rSNPs	diseases
2	esv3330182	chr17:15652014-16569534	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
3	esv3446844	chr17:15654843-16572246	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	177 gene(s)	inside rSNPs	diseases
4	nsv1063459	chr17:15804228-16543593	Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	164 gene(s)	inside rSNPs	diseases
5	nsv522169	chr17:15923709-16147821	Strong transcription Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv907715	chr17:16019978-16206540	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
7	nsv907717	chr17:16076898-16239832	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
8	nsv528263	chr17:16097430-16196996	Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers 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	41 gene(s)	inside rSNPs	diseases
9	esv3326983	chr17:16138963-16210147	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs12946619	TTC19	cis	lymphoblastoid	seeQTL
rs12946619	ADORA2B	cis	Thyroid	GTEx
rs12946619	ADORA2B	cis	Muscle Skeletal	GTEx
rs12946619	ADORA2B	cis	Esophagus Muscularis	GTEx
rs12946619	ZSWIM7	Cis_1M	lymphoblastoid	RTeQTL
rs12946619	ADORA2B	cis	Artery Tibial	GTEx
rs12946619	ADORA2B	cis	Adipose Subcutaneous	GTEx
rs12946619	CENPV	cis	lymphoblastoid	seeQTL
rs12946619	ZSWIM7	cis	Muscle Skeletal	GTEx
rs12946619	TTC19	Cis_1M	lymphoblastoid	RTeQTL
rs12946619	NCOR1	Cis_1M	lymphoblastoid	RTeQTL
rs12946619	ADORA2B	cis	Nerve Tibial	GTEx
rs12946619	CENPV	cis	Artery Tibial	GTEx

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:16121000-16163200	Weak transcription	Spleen	Spleen
2	chr17:16121200-16157000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr17:16121200-16158800	Weak transcription	Left Ventricle	heart
4	chr17:16121200-16159800	Weak transcription	Lung	lung
5	chr17:16121200-16163000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr17:16121400-16158600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr17:16121400-16158800	Weak transcription	Fetal Muscle Leg	muscle
8	chr17:16121400-16159000	Weak transcription	Fetal Muscle Trunk	muscle
9	chr17:16121400-16170600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr17:16121600-16147000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr17:16121600-16150200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr17:16121600-16151800	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr17:16121600-16158400	Weak transcription	Brain Hippocampus Middle	brain
14	chr17:16121600-16158600	Weak transcription	Brain Germinal Matrix	brain
15	chr17:16121800-16150200	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr17:16121800-16153600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr17:16121800-16158200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr17:16121800-16158400	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr17:16121800-16163200	Weak transcription	Primary hematopoietic stem cells	blood
20	chr17:16121800-16163200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr17:16122000-16163400	Weak transcription	Fetal Brain Female	brain
22	chr17:16122200-16146800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr17:16122200-16150200	Weak transcription	Liver	Liver
24	chr17:16123000-16154200	Weak transcription	Ovary	ovary
25	chr17:16124200-16158200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr17:16126200-16163200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr17:16126200-16163400	Weak transcription	Primary B cells from cord blood	blood
28	chr17:16126400-16158800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr17:16126600-16153800	Weak transcription	A549	lung
30	chr17:16127600-16158600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr17:16127800-16147000	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr17:16130400-16147000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr17:16132200-16163200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr17:16132400-16163600	Weak transcription	HSMM	muscle
35	chr17:16132600-16147000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr17:16133200-16147000	Weak transcription	NH-A	brain
37	chr17:16133200-16153800	Weak transcription	Hela-S3	cervix
38	chr17:16133400-16146800	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr17:16133800-16163000	Weak transcription	Fetal Thymus	thymus
40	chr17:16133800-16176200	Weak transcription	NHEK	skin
41	chr17:16134000-16147000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr17:16134000-16147000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr17:16134000-16147200	Weak transcription	NHDF-Ad	bronchial
44	chr17:16134000-16170600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr17:16134200-16147000	Weak transcription	GM12878-XiMat	blood
46	chr17:16134200-16162400	Weak transcription	Dnd41	blood
47	chr17:16134400-16163200	Weak transcription	Thymus	Thymus
48	chr17:16134800-16163200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr17:16135400-16150200	Weak transcription	Colonic Mucosa	Colon
50	chr17:16135600-16158600	Weak transcription	Adipose Nuclei	Adipose

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links