Variant report

Variant	rs12604067
Chromosome Location	chr17:33952103-33952104
allele	C/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:

Variant related genes	Relation type
ENSG00000006125	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1001441	0.84[JPT][hapmap]
rs10068	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs1037590	0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1037592	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10512472	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap]
rs1071965	0.81[CHB][hapmap]
rs11653310	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs11653357	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11655098	0.82[CEU][hapmap]
rs11655803	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11656138	0.83[ASN][1000 genomes]
rs11868206	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12452797	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs12940584	0.82[CEU][hapmap]
rs12943224	0.82[CEU][hapmap]
rs12947592	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12948669	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1671656	0.84[ASN][1000 genomes]
rs16971217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16971227	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17606150	0.82[CEU][hapmap]
rs17637907	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs17669281	0.82[CEU][hapmap]
rs17670584	0.82[CEU][hapmap]
rs225243	0.84[ASN][1000 genomes]
rs225247	0.91[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs225251	0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs225254	0.90[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs225259	0.81[ASN][1000 genomes]
rs225262	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs225277	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs225295	0.82[ASN][1000 genomes]
rs225304	0.83[ASN][1000 genomes]
rs225306	0.85[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2840044	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs2889311	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35237539	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7213476	0.91[ASN][1000 genomes]
rs9890191	0.98[ASN][1000 genomes]
rs9891574	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9897552	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9899860	0.99[ASN][1000 genomes]
rs9899927	0.99[ASN][1000 genomes]
rs9900378	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9902765	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9907772	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9913875	0.99[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

No data

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	chr17:33926800-33952600	Weak transcription	Fetal Brain Male	brain
8	chr17:33931000-34040200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr17:33933000-33967400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr17:33933000-33997800	Weak transcription	Esophagus	oesophagus
11	chr17:33933600-33952800	Weak transcription	Brain Substantia Nigra	brain
12	chr17:33933600-33967400	Weak transcription	Gastric	stomach
13	chr17:33935600-33953000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr17:33935600-33953400	Weak transcription	HSMMtube	muscle
15	chr17:33936000-33953800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr17:33936800-33956800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr17:33937400-33965000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr17:33938200-33953200	Weak transcription	Colonic Mucosa	Colon
19	chr17:33938600-33952800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr17:33938600-33953400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr17:33938600-33953600	Weak transcription	Spleen	Spleen
22	chr17:33938600-33954600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr17:33939000-33953800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr17:33940000-33960000	Weak transcription	Right Ventricle	heart
25	chr17:33942200-33953000	Weak transcription	NHLF	lung
26	chr17:33942200-33953400	Weak transcription	Lung	lung
27	chr17:33942200-33954400	Weak transcription	Aorta	Aorta
28	chr17:33943400-33956800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr17:33943600-33956800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr17:33944600-33957400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr17:33945600-33953800	Weak transcription	Fetal Heart	heart
32	chr17:33947000-33958200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr17:33947400-33952800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr17:33947800-33952400	Weak transcription	Fetal Stomach	stomach
35	chr17:33947800-33953600	Weak transcription	Fetal Intestine Small	intestine
36	chr17:33947800-33955000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr17:33948400-33973400	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr17:33948600-33958200	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr17:33948600-33973600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr17:33948800-34010600	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr17:33949000-33986400	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr17:33949200-33953600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr17:33949200-34001200	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr17:33949400-33953600	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr17:33949800-33958800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr17:33950000-33957200	Strong transcription	Osteobl	bone
47	chr17:33950200-33957200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr17:33950200-33957800	Strong transcription	Brain Inferior Temporal Lobe	brain
49	chr17:33950400-33953800	Strong transcription	Primary B cells from peripheral blood	blood
50	chr17:33950400-33957400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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