Variant report

Variant	rs11650043
Chromosome Location	chr17:46027852-46027853
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	chr17:46025886-46028079	HepG2	liver:	n/a	n/a
2	POLR2A	chr17:46025867-46027977	MCF-7	breast:	n/a	n/a
3	SMC3	chr17:46025869-46027855	SK-N-SH	brain:	n/a	chr17:46026781-46026795
4	CTCF	chr17:46025931-46027875	A549	lung:	n/a	chr17:46026781-46026802 chr17:46026782-46026795 chr17:46026780-46026796 chr17:46026779-46026797
5	POLR2A	chr17:46025923-46028067	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:46026192..46029068-chr17:46087372..46089166,2	K562	blood:
2	chr17:46027611..46030432-chr17:46048552..46050466,2	K562	blood:
3	chr17:46023026..46029175-chr17:46044937..46051234,10	K562	blood:
4	chr17:45968434..45977260-chr17:46017847..46029594,27	MCF-7	breast:
5	chr17:46027110..46029262-chr17:46094448..46097370,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000264019	TF binding region
ENSG00000167182	Chromatin interaction
ENSG00000264920	Chromatin interaction
ENSG00000108465	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10491182	1.00[CEU][hapmap];0.87[GIH][hapmap]
rs10491183	1.00[CEU][hapmap];0.87[GIH][hapmap]
rs11650304	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11651275	1.00[CEU][hapmap]
rs16949676	1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17617360	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs17618704	1.00[CEU][hapmap];0.81[GIH][hapmap];0.85[MEX][hapmap]
rs17679445	1.00[CEU][hapmap];0.81[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs41429650	1.00[CEU][hapmap];0.87[GIH][hapmap]
rs4378657	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7209072	1.00[CEU][hapmap];0.87[GIH][hapmap]
rs7210041	1.00[CEU][hapmap]
rs9895554	1.00[CEU][hapmap];0.82[GIH][hapmap]
rs9900074	1.00[CEU][hapmap]
rs9903963	1.00[CEU][hapmap];0.87[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv518892	chr17:45887951-46029432	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv908575	chr17:45957591-46049533	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
4	esv1000014	chr17:46019228-46029457	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11650043	PNPO	Cis_1M	lymphoblastoid	RTeQTL
rs11650043	SKAP1	cis	lymphoblastoid	seeQTL

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46019800-46034200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr17:46019800-46047600	Weak transcription	Aorta	Aorta
3	chr17:46020000-46034600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr17:46023200-46030000	Genic enhancers	Fetal Intestine Large	intestine
5	chr17:46024400-46031600	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr17:46026000-46028000	Enhancers	Esophagus	oesophagus
7	chr17:46026200-46028000	Genic enhancers	Sigmoid Colon	Sigmoid Colon
8	chr17:46026400-46028000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr17:46026400-46028000	Enhancers	Placenta	Placenta
10	chr17:46027000-46028000	Enhancers	Placenta Amnion	Placenta Amnion
11	chr17:46027000-46030000	Weak transcription	Psoas Muscle	Psoas
12	chr17:46027200-46028000	Enhancers	Primary hematopoietic stem cells	blood
13	chr17:46027200-46028000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr17:46027200-46028000	Enhancers	Primary T helper naive cells from peripheral blood	blood
15	chr17:46027200-46028000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr17:46027200-46028000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr17:46027200-46028200	Enhancers	Primary T cells fromperipheralblood	blood
18	chr17:46027200-46028200	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr17:46027200-46028200	Enhancers	Fetal Thymus	thymus
20	chr17:46027200-46029200	Genic enhancers	Fetal Intestine Small	intestine
21	chr17:46027200-46030000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr17:46027200-46031200	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr17:46027200-46032600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr17:46027200-46034400	Weak transcription	Hela-S3	cervix
25	chr17:46027200-46047200	Weak transcription	Spleen	Spleen
26	chr17:46027400-46028000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr17:46027400-46028000	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr17:46027400-46028000	Enhancers	Thymus	Thymus
29	chr17:46027400-46028200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr17:46027400-46028200	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr17:46027400-46028200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr17:46027400-46028400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr17:46027400-46028400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr17:46027400-46029600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr17:46027400-46029600	Weak transcription	Lung	lung
36	chr17:46027400-46030000	Weak transcription	Rectal Smooth Muscle	rectum
37	chr17:46027400-46030000	Genic enhancers	Stomach Mucosa	stomach
38	chr17:46027400-46030800	Strong transcription	Fetal Stomach	stomach
39	chr17:46027400-46032600	Weak transcription	NHLF	lung
40	chr17:46027400-46033800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr17:46027400-46033800	Weak transcription	NHDF-Ad	bronchial
42	chr17:46027400-46034000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr17:46027400-46034200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr17:46027400-46034400	Weak transcription	Fetal Lung	lung
45	chr17:46027400-46034600	Weak transcription	K562	blood
46	chr17:46027400-46034800	Weak transcription	NH-A	brain
47	chr17:46027600-46028000	Strong transcription	NHEK	skin
48	chr17:46027600-46028200	Enhancers	GM12878-XiMat	blood
49	chr17:46027600-46028200	Enhancers	HMEC	breast
50	chr17:46027600-46028600	Weak transcription	Primary monocytes fromperipheralblood	blood

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