Variant report

Variant	rs226428
Chromosome Location	chr17:34049950-34049951
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:34048945..34052195-chr17:34055634..34059515,4	K562	blood:
2	chr17:34048477..34051803-chr17:34054688..34058128,3	K562	blood:

Variant related genes	Relation type
ENSG00000141150	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1049379	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12150359	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1476553	0.94[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs161182	0.82[EUR][1000 genomes]
rs161183	0.84[EUR][1000 genomes]
rs161184	0.82[EUR][1000 genomes]
rs1634684	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs225245	0.85[CEU][hapmap];0.82[TSI][hapmap]
rs225255	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs225269	0.88[EUR][1000 genomes]
rs225272	0.88[EUR][1000 genomes]
rs225273	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs225281	0.89[EUR][1000 genomes]
rs225282	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs225284	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]
rs225290	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs225293	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs225297	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]
rs225299	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs225302	0.83[EUR][1000 genomes]
rs226088	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs226426	0.83[ASW][hapmap];0.87[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs226429	0.82[ASN][1000 genomes]
rs226432	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs226434	0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap]
rs226439	0.83[ASW][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.95[JPT][hapmap]
rs226441	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2285742	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2301730	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs321596	0.81[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap]
rs321599	0.81[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap]
rs321601	0.94[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap]
rs321616	0.81[CEU][hapmap]
rs321617	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs321618	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.84[EUR][1000 genomes]
rs3890901	0.96[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4796103	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6505489	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6505490	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6505491	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6505492	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6505493	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs71366475	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs720774	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7217565	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7221081	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7221096	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7406966	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes]
rs8064556	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8067294	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8073375	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8078905	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9635770	0.87[EUR][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	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs226428	TBC1D29	cis	parietal	SCAN
rs226428	SLFN5	cis	parietal	SCAN
rs226428	PEX12	cis	cerebellum	SCAN
rs226428	AP2B1	cis	Muscle Skeletal	GTEx
rs226428	TBC1D29	cis	cerebellum	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	chr17:34018800-34050600	Weak transcription	Esophagus	oesophagus
3	chr17:34023200-34051600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr17:34024200-34056200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr17:34026600-34050200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr17:34032600-34055800	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr17:34034800-34053400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr17:34034800-34055600	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr17:34035400-34056200	Strong transcription	A549	lung
10	chr17:34035800-34053000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr17:34036000-34055600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr17:34036400-34052200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr17:34036600-34055800	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr17:34036800-34054800	Strong transcription	Primary B cells from peripheral blood	blood
15	chr17:34037000-34053000	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr17:34040000-34052800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr17:34040200-34055000	Strong transcription	Rectal Mucosa Donor 31	rectum
18	chr17:34040400-34054400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr17:34040600-34050800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr17:34040600-34054800	Strong transcription	Primary T cells fromperipheralblood	blood
21	chr17:34040600-34055200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr17:34040600-34055600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr17:34040800-34050200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr17:34040800-34050600	Weak transcription	Stomach Mucosa	stomach
25	chr17:34040800-34053400	Strong transcription	Duodenum Mucosa	Duodenum
26	chr17:34040800-34054400	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr17:34040800-34054400	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr17:34040800-34055000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr17:34040800-34055000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr17:34041000-34050200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr17:34041400-34053000	Weak transcription	Right Atrium	heart
32	chr17:34042000-34050600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr17:34042400-34053000	Strong transcription	K562	blood
34	chr17:34042600-34052000	Strong transcription	Fetal Muscle Leg	muscle
35	chr17:34042800-34052000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr17:34042800-34055400	Strong transcription	Primary T cells from cord blood	blood
37	chr17:34043000-34050400	Weak transcription	Brain Substantia Nigra	brain
38	chr17:34043000-34052600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr17:34043600-34052800	Strong transcription	HSMM	muscle
40	chr17:34043600-34053800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr17:34043800-34050600	Weak transcription	Pancreas	Pancrea
42	chr17:34043800-34054600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr17:34044200-34050600	Weak transcription	Right Ventricle	heart
44	chr17:34044600-34050000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr17:34044800-34050000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr17:34044800-34050000	Weak transcription	NHEK	skin
47	chr17:34044800-34050200	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr17:34044800-34050200	Weak transcription	Ovary	ovary
49	chr17:34044800-34050600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr17:34044800-34050600	Weak transcription	Colon Smooth Muscle	Colon

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