Variant report

Variant	rs225297
Chromosome Location	chr17:33924587-33924588
allele	C/T
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	chr17:33923089-33925722	K562	blood:	n/a	n/a
2	POLR2A	chr17:33924324-33924606	K562	blood:	n/a	n/a
3	POLR2A	chr17:33923692-33926254	A549	lung:	n/a	n/a
4	POLR2A	chr17:33923040-33925467	K562	blood:	n/a	n/a
5	POLR2A	chr17:33923474-33925473	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr17:33923083-33926653	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:33922858..33924678-chr17:34135851..34137902,2	K562	blood:

Variant related genes	Relation type
ENSG00000267592	TF binding region
ENSG00000267578	Chromatin interaction
ENSG00000172660	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1049379	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12150359	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1476553	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs161182	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs161183	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs161184	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1634684	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs167691	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs178649	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2124246	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2124247	0.84[ASN][1000 genomes]
rs225245	0.89[CEU][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs225255	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs225269	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs225272	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs225273	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs225281	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs225282	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs225284	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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225290	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225293	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225299	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225302	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs226088	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs226426	0.87[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs226428	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes]
rs226432	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs226434	0.82[ASW][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs226439	0.91[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs226441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2285742	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2301730	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs321596	0.85[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs321599	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs321601	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs321607	0.81[CEU][hapmap];0.83[ASN][1000 genomes]
rs321608	0.83[ASN][1000 genomes]
rs321616	0.85[CEU][hapmap]
rs321617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs321618	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3890901	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4796103	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6505489	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6505490	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6505491	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6505492	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6505493	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs71366475	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs720774	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7217565	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7221081	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7221096	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7406966	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8064556	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8067294	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8073375	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8078905	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9635770	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]

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	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	nsv908079	chr17:33849869-34034851	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
3	nsv1060890	chr17:33884124-34011034	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	nsv543318	chr17:33884124-34011034	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs225297	TBC1D29	cis	cerebellum	SCAN
rs225297	TBC1D29	cis	parietal	SCAN
rs225297	SLFN5	cis	parietal	SCAN
rs225297	PEX12	cis	cerebellum	SCAN
rs225297	AP2B1	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:33915200-33930600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr17:33915200-33932600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr17:33915600-33954600	Weak transcription	Small Intestine	intestine
4	chr17:33916000-33942000	Weak transcription	Right Atrium	heart
5	chr17:33916400-33944800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr17:33916800-33924600	Weak transcription	Brain Substantia Nigra	brain
7	chr17:33916800-33925200	Weak transcription	Fetal Brain Male	brain
8	chr17:33916800-33925200	Weak transcription	Fetal Kidney	kidney
9	chr17:33916800-33945400	Weak transcription	Stomach Mucosa	stomach
10	chr17:33916800-34001200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr17:33917600-33934600	Weak transcription	Brain Angular Gyrus	brain
12	chr17:33919400-33940000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr17:33919600-33931000	Strong transcription	K562	blood
14	chr17:33920000-33937400	Strong transcription	A549	lung
15	chr17:33920400-33936400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr17:33920600-33926600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr17:33920600-33939800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr17:33920600-33939800	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr17:33920600-33939800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr17:33920600-33940000	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr17:33920600-33940200	Strong transcription	Primary B cells from peripheral blood	blood
22	chr17:33920600-33942200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr17:33920600-33942800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr17:33920600-33944000	Strong transcription	Dnd41	blood
25	chr17:33920600-33969800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr17:33920800-33926200	Strong transcription	Primary B cells from cord blood	blood
27	chr17:33920800-33931000	Strong transcription	GM12878-XiMat	blood
28	chr17:33920800-33931000	Strong transcription	Osteobl	bone
29	chr17:33920800-33938400	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr17:33920800-33975800	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr17:33921000-33925800	Strong transcription	Hela-S3	cervix
32	chr17:33921000-33926600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr17:33921000-33926800	Strong transcription	HMEC	breast
34	chr17:33921000-33930600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr17:33921000-33930800	Strong transcription	Muscle Satellite Cultured Cells	--
36	chr17:33921000-33930800	Strong transcription	NH-A	brain
37	chr17:33921000-33931400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr17:33921000-33931600	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr17:33921000-33932000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr17:33921000-33937200	Strong transcription	Placenta	Placenta
41	chr17:33921000-33939800	Strong transcription	Primary T helper cells fromperipheralblood	blood
42	chr17:33921000-33939800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr17:33921000-33940400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr17:33921000-33941400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr17:33921000-33942200	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr17:33921000-33943000	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr17:33921000-33946200	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr17:33921000-33946600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr17:33921000-34024400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr17:33921200-33924800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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