Variant report

Variant	rs225254
Chromosome Location	chr17:33953384-33953385
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:33948219..33950290-chr17:33951562..33953635,2	K562	blood:
2	chr17:33952642..33955408-chr17:33957507..33960024,3	K562	blood:

Variant related genes	Relation type
ENSG00000006125	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10068	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1037590	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs1037592	0.83[ASN][1000 genomes]
rs10512472	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs11080357	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11653310	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11653357	0.83[ASN][1000 genomes]
rs11655803	0.84[ASN][1000 genomes]
rs11656138	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12452797	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs12604067	0.90[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs12947592	0.83[ASN][1000 genomes]
rs12948669	0.83[ASN][1000 genomes]
rs1671656	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16971217	0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs16971227	0.84[ASN][1000 genomes]
rs17637907	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs225243	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225247	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225251	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225259	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs225262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs225277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs225285	0.89[CEU][hapmap]
rs225295	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs225304	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs225306	0.82[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.86[YRI][hapmap];0.98[ASN][1000 genomes]
rs2840044	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28667378	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35237539	0.83[ASN][1000 genomes]
rs7212704	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8069037	0.93[AFR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8073935	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9890191	0.82[ASN][1000 genomes]
rs9891574	0.83[ASN][1000 genomes]
rs9891800	0.90[EUR][1000 genomes]
rs9897552	0.85[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs9899860	0.83[ASN][1000 genomes]
rs9899927	0.83[ASN][1000 genomes]
rs9900378	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9902765	0.81[ASN][1000 genomes]
rs9907772	0.81[ASN][1000 genomes]
rs9908158	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9913003	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9913875	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv1062793	chr17:33944732-33976685	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs225254	CCL14-CCL15	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:33915600-33954600	Weak transcription	Small Intestine	intestine
2	chr17:33916800-34001200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr17:33920600-33969800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr17:33920800-33975800	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr17:33921000-34024400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr17:33926000-33955200	Weak transcription	Pancreas	Pancrea
7	chr17:33931000-34040200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr17:33933000-33967400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr17:33933000-33997800	Weak transcription	Esophagus	oesophagus
10	chr17:33933600-33967400	Weak transcription	Gastric	stomach
11	chr17:33935600-33953400	Weak transcription	HSMMtube	muscle
12	chr17:33936000-33953800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr17:33936800-33956800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr17:33937400-33965000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr17:33938600-33953400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr17:33938600-33953600	Weak transcription	Spleen	Spleen
17	chr17:33938600-33954600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr17:33939000-33953800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr17:33940000-33960000	Weak transcription	Right Ventricle	heart
20	chr17:33942200-33953400	Weak transcription	Lung	lung
21	chr17:33942200-33954400	Weak transcription	Aorta	Aorta
22	chr17:33943400-33956800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr17:33943600-33956800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr17:33944600-33957400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr17:33945600-33953800	Weak transcription	Fetal Heart	heart
26	chr17:33947000-33958200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr17:33947800-33953600	Weak transcription	Fetal Intestine Small	intestine
28	chr17:33947800-33955000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr17:33948400-33973400	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr17:33948600-33958200	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr17:33948600-33973600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr17:33948800-34010600	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr17:33949000-33986400	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr17:33949200-33953600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr17:33949200-34001200	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr17:33949400-33953600	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr17:33949800-33958800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr17:33950000-33957200	Strong transcription	Osteobl	bone
39	chr17:33950200-33957200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr17:33950200-33957800	Strong transcription	Brain Inferior Temporal Lobe	brain
41	chr17:33950400-33953800	Strong transcription	Primary B cells from peripheral blood	blood
42	chr17:33950400-33957400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr17:33950400-33965400	Strong transcription	HSMM	muscle
44	chr17:33950600-33957200	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr17:33950600-33957200	Strong transcription	HMEC	breast
46	chr17:33950600-33957200	Strong transcription	NHDF-Ad	bronchial
47	chr17:33950600-33958200	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr17:33950600-33959000	Strong transcription	Placenta	Placenta
49	chr17:33950600-33959000	Strong transcription	Stomach Smooth Muscle	stomach
50	chr17:33950600-33968600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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