Variant report

Variant	rs11650615
Chromosome Location	chr17:46123698-46123699
allele	C/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	MXI1	chr17:46121714-46126967	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr17:46122734-46126909	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr17:46122485-46124228	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr17:46123662-46123940	ECC-1	luminal epithelium:	n/a	n/a
5	POLR2A	chr17:46123586-46123834	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr17:46122512-46124013	PFSK-1	brain:	n/a	n/a
7	POLR2A	chr17:46123447-46126752	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr17:46121736-46126744	K562	blood:	n/a	n/a
9	JUN	chr17:46122472-46126784	K562	blood:	n/a	chr17:46125601-46125610 chr17:46125499-46125508 chr17:46124562-46124569 chr17:46124562-46124571 chr17:46125676-46125685 chr17:46124353-46124365

No.	Distal block	Cell Line	Cell type
1	chr17:46123351..46126971-chr17:46177351..46182209,7	K562	blood:
2	chr17:46120800..46123915-chr17:46177973..46180193,3	MCF-7	breast:
3	chr17:46052757..46054496-chr17:46123061..46125014,2	K562	blood:
4	chr17:46123538..46128867-chr17:46183649..46187295,7	MCF-7	breast:
5	chr17:46122869..46127022-chr17:46176971..46180616,11	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-COPZ2-1	chr17:46122503-46125412	ENSG00000263412.1

Variant related genes	Relation type
NFE2L1	TF binding region
ENSG00000108465	Chromatin interaction
ENSG00000108468	Chromatin interaction
ENSG00000002919	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10514938	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11079810	0.92[YRI][hapmap]
rs11079813	0.87[LWK][hapmap];0.82[MKK][hapmap];0.92[YRI][hapmap]
rs11654292	0.91[YRI][hapmap]
rs11654342	0.88[AFR][1000 genomes]
rs11658242	0.88[LWK][hapmap];0.84[MKK][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes]
rs12103808	0.80[AFR][1000 genomes]
rs12951323	1.00[JPT][hapmap]
rs16948835	1.00[CHB][hapmap]
rs16952265	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16953235	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16953382	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16953461	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16953925	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16954078	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16954204	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1975703	0.92[YRI][hapmap]
rs41280120	1.00[ASN][1000 genomes]
rs41336845	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4794321	1.00[JPT][hapmap]
rs6504067	0.92[YRI][hapmap]
rs6504115	0.92[YRI][hapmap]
rs7207553	0.86[YRI][hapmap]
rs7210671	0.92[YRI][hapmap]
rs7216504	1.00[ASN][1000 genomes]
rs7221897	0.88[YRI][hapmap]
rs7222646	0.88[LWK][hapmap];0.82[MKK][hapmap];0.92[YRI][hapmap]
rs7224155	0.87[LWK][hapmap];0.82[MKK][hapmap];0.92[YRI][hapmap]
rs72823527	1.00[ASN][1000 genomes]
rs72823530	1.00[ASN][1000 genomes]
rs72823534	1.00[ASN][1000 genomes]
rs72823591	1.00[ASN][1000 genomes]
rs72823599	1.00[ASN][1000 genomes]
rs72823601	1.00[ASN][1000 genomes]
rs72825504	1.00[ASN][1000 genomes]
rs72825512	1.00[ASN][1000 genomes]
rs72825517	1.00[ASN][1000 genomes]
rs72825548	1.00[ASN][1000 genomes]
rs72825584	1.00[ASN][1000 genomes]
rs8065797	0.92[YRI][hapmap];0.88[AFR][1000 genomes]
rs8067005	1.00[ASN][1000 genomes]
rs8067216	0.87[EUR][1000 genomes]
rs8067470	0.82[MKK][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes]
rs8071697	0.88[YRI][hapmap]
rs8073220	0.83[AFR][1000 genomes]
rs8073371	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9893110	0.92[YRI][hapmap]
rs9895554	0.83[LWK][hapmap];0.95[MKK][hapmap];0.88[YRI][hapmap]
rs9900074	0.83[YRI][hapmap]
rs9905800	0.88[LWK][hapmap];0.84[MKK][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes]
rs9909922	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469808	chr17:46049868-46228673	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv482897	chr17:46049868-46228673	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs11650615	CDK5RAP3	cis	parietal	SCAN
rs11650615	AOC3	cis	parietal	SCAN
rs11650615	PNPO	cis	parietal	SCAN
rs11650615	SKAP1	Cis_1M	lymphoblastoid	RTeQTL
rs11650615	SNX11	cis	cerebellum	SCAN
rs11650615	C17orf57	cis	parietal	SCAN
rs11650615	CDK5RAP3	cis	Artery Tibial	GTEx
rs11650615	KRT17	cis	cerebellum	SCAN
rs11650615	DBF4B	cis	cerebellum	SCAN
rs11650615	G6PC	cis	parietal	SCAN
rs11650615	CDK5RAP3	cis	cerebellum	SCAN
rs11650615	G6PC	cis	cerebellum	SCAN
rs11650615	CDK5RAP3	cis	Nerve Tibial	GTEx

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46115600-46123800	Weak transcription	Brain Substantia Nigra	brain
2	chr17:46116000-46124000	Weak transcription	Brain Hippocampus Middle	brain
3	chr17:46119400-46123800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr17:46120600-46124200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr17:46120600-46124200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr17:46121800-46124400	Enhancers	Fetal Muscle Leg	muscle
7	chr17:46122400-46124000	Weak transcription	Primary T cells from cord blood	blood
8	chr17:46122400-46124200	Enhancers	Fetal Muscle Trunk	muscle
9	chr17:46122400-46124400	Enhancers	Adipose Nuclei	Adipose
10	chr17:46122600-46124000	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr17:46122600-46124000	Enhancers	Esophagus	oesophagus
12	chr17:46122600-46124000	Enhancers	HMEC	breast
13	chr17:46122600-46124200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr17:46122600-46124200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr17:46122600-46124400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr17:46122600-46124800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr17:46122600-46124800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
18	chr17:46122600-46124800	Flanking Active TSS	HSMM	muscle
19	chr17:46122600-46125000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr17:46122800-46123800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr17:46122800-46123800	Enhancers	Breast Myoepithelial Primary Cells	Breast
22	chr17:46122800-46123800	Enhancers	Hela-S3	cervix
23	chr17:46122800-46124000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr17:46122800-46124000	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr17:46122800-46124000	Enhancers	Fetal Heart	heart
26	chr17:46122800-46124200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr17:46122800-46124200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr17:46122800-46124200	Enhancers	Fetal Thymus	thymus
29	chr17:46122800-46124200	Enhancers	Stomach Smooth Muscle	stomach
30	chr17:46122800-46124400	Enhancers	Colonic Mucosa	Colon
31	chr17:46122800-46124400	Enhancers	Rectal Mucosa Donor 31	rectum
32	chr17:46122800-46124400	Enhancers	Right Atrium	heart
33	chr17:46122800-46124600	Enhancers	Pancreas	Pancrea
34	chr17:46122800-46124600	Enhancers	Placenta Amnion	Placenta Amnion
35	chr17:46122800-46124600	Enhancers	HepG2	liver
36	chr17:46122800-46124800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr17:46122800-46125000	Flanking Active TSS	NHEK	skin
38	chr17:46123000-46124000	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr17:46123000-46124000	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr17:46123000-46124000	Weak transcription	Brain Anterior Caudate	brain
41	chr17:46123000-46124200	Enhancers	Primary B cells from cord blood	blood
42	chr17:46123000-46124200	Enhancers	Brain Germinal Matrix	brain
43	chr17:46123000-46124200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr17:46123000-46124400	Enhancers	Fetal Intestine Small	intestine
45	chr17:46123000-46124600	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr17:46123000-46124800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr17:46123200-46123800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr17:46123200-46123800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr17:46123200-46124000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr17:46123200-46124000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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