Variant report

Variant	rs4795086
Chromosome Location	chr17:34042190-34042191
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	EP300	chr17:34041803-34042361	SK-N-SH_RA	brain:	n/a	n/a
2	GATA3	chr17:34041854-34042364	SH-SY5Y	brain:	n/a	n/a
3	PBX3	chr17:34041941-34042406	SK-N-SH	brain:	n/a	n/a
4	POLR2A	chr17:34042062-34042387	SK-N-SH	brain:	n/a	n/a
5	EP300	chr17:34041532-34042569	SK-N-SH	brain:	n/a	chr17:34042364-34042378
6	EP300	chr17:34041829-34042380	SK-N-SH_RA	brain:	n/a	chr17:34042364-34042378
7	POLR2A	chr17:34042154-34042334	K562	blood:	n/a	n/a
8	GATA3	chr17:34041821-34042503	SK-N-SH	brain:	n/a	n/a
9	GATA2	chr17:34041988-34042345	SH-SY5Y	brain:	n/a	n/a
10	GATA3	chr17:34041709-34042545	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
RPL17P42	TF binding region

Extended variants
information (count: 107 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10438814	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1080352	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11080356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap]
rs11650473	1.00[CHB][hapmap]
rs11871358	0.81[EUR][1000 genomes]
rs1634683	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17550268	0.81[CEU][hapmap]
rs17550632	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17550716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap]
rs17638867	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs178736	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs188959	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2011528	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2011897	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225244	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs225246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs225248	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs225249	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs225250	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs225252	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs225256	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs225257	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs225258	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs225260	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs225261	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs225264	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs225265	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs225266	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs225267	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs225268	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs225270	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs225271	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs225274	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs225275	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs225276	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs225278	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs225279	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs225283	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs225285	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs225286	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs225287	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs225288	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs225292	0.82[EUR][1000 genomes]
rs225294	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs225296	0.91[EUR][1000 genomes]
rs225298	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs225300	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs225303	0.90[EUR][1000 genomes]
rs225305	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs225306	0.90[CEU][hapmap]
rs225307	0.91[EUR][1000 genomes]
rs225308	0.91[EUR][1000 genomes]
rs226084	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs226087	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs226089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs226090	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2376177	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2428464	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2523114	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2523116	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2523117	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2626625	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2626626	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3859282	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3859284	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3890900	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4796098	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[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4796100	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4796101	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4796104	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6505484	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6505485	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6505486	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6505487	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7208672	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7210966	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7211724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7213804	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7214250	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7214742	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7217378	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7217533	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7221203	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72829922	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72829923	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72829925	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72829927	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72829932	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72829933	0.87[EUR][1000 genomes]
rs72829936	0.82[EUR][1000 genomes]
rs72829940	0.82[EUR][1000 genomes]
rs8064895	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8070030	1.00[CHB][hapmap]
rs8071584	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8072676	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8074800	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8077826	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9303690	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9674851	1.00[JPT][hapmap]
rs9894813	0.80[CEU][hapmap];1.00[CHD][hapmap]
rs9895464	1.00[JPT][hapmap]
rs9898128	1.00[JPT][hapmap]
rs9912939	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9914929	1.00[JPT][hapmap]

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	nsv534371	chr17:33456878-34094068	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
2	nsv908080	chr17:34027964-34054044	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4795086	LOC645744	Cis_1M	lymphoblastoid	RTeQTL
rs4795086	SUZ12P	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:33968000-34055800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr17:33999400-34043400	Weak transcription	Fetal Brain Male	brain
3	chr17:34018800-34050600	Weak transcription	Esophagus	oesophagus
4	chr17:34019000-34044000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr17:34022200-34042400	Weak transcription	Aorta	Aorta
6	chr17:34023200-34043800	Weak transcription	Spleen	Spleen
7	chr17:34023200-34044000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr17:34023200-34051600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr17:34023400-34044200	Weak transcription	Brain Germinal Matrix	brain
10	chr17:34024200-34056200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr17:34026600-34050200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr17:34032600-34055800	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr17:34034800-34053400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr17:34034800-34055600	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr17:34035400-34056200	Strong transcription	A549	lung
16	chr17:34035800-34053000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr17:34036000-34045800	Strong transcription	Fetal Muscle Trunk	muscle
18	chr17:34036000-34047400	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr17:34036000-34049000	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr17:34036000-34055600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr17:34036200-34044000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr17:34036400-34042600	Weak transcription	Gastric	stomach
23	chr17:34036400-34042600	Weak transcription	Pancreas	Pancrea
24	chr17:34036400-34052200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr17:34036600-34055800	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr17:34036800-34054800	Strong transcription	Primary B cells from peripheral blood	blood
27	chr17:34037000-34047400	Strong transcription	Primary B cells from cord blood	blood
28	chr17:34037000-34053000	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr17:34037200-34042600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr17:34037200-34044000	Weak transcription	Colon Smooth Muscle	Colon
31	chr17:34037200-34044800	Strong transcription	HMEC	breast
32	chr17:34038000-34044000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr17:34038400-34042200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr17:34038400-34042400	Weak transcription	Brain Cingulate Gyrus	brain
35	chr17:34038400-34042400	Weak transcription	Brain Hippocampus Middle	brain
36	chr17:34038600-34043400	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr17:34039000-34042600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr17:34039000-34043600	Weak transcription	Brain Angular Gyrus	brain
39	chr17:34039400-34044200	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr17:34039600-34043600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr17:34039800-34045200	Strong transcription	GM12878-XiMat	blood
42	chr17:34039800-34045800	Genic enhancers	Adipose Nuclei	Adipose
43	chr17:34040000-34043000	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr17:34040000-34043000	Enhancers	Brain Anterior Caudate	brain
45	chr17:34040000-34052800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr17:34040200-34042800	Genic enhancers	Primary T cells from cord blood	blood
47	chr17:34040200-34055000	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr17:34040400-34042200	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr17:34040400-34043200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr17:34040400-34043400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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