Variant report

Variant	rs17100621
Chromosome Location	chr12:65133461-65133462
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:65130397..65134175-chr12:65151034..65153739,3	MCF-7	breast:
2	chr12:65118320..65120972-chr12:65132835..65135195,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135677	Chromatin interaction
ENSG00000215159	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs17100619	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs17100633	1.00[MEX][hapmap]
rs17100642	1.00[MEX][hapmap]
rs2230292	0.92[YRI][hapmap];0.80[AFR][1000 genomes]
rs55747137	1.00[AMR][1000 genomes]
rs56739324	1.00[AMR][1000 genomes]
rs58327448	1.00[AMR][1000 genomes]
rs58606781	1.00[AMR][1000 genomes]
rs60988778	1.00[AMR][1000 genomes]
rs74098127	0.98[AFR][1000 genomes]
rs74098643	0.80[AFR][1000 genomes]
rs74099588	1.00[AMR][1000 genomes]
rs74099656	1.00[AMR][1000 genomes]
rs74099664	1.00[AMR][1000 genomes]
rs74099673	1.00[AMR][1000 genomes]
rs74099678	1.00[AMR][1000 genomes]
rs74099681	1.00[AMR][1000 genomes]
rs74099691	1.00[AMR][1000 genomes]
rs74099695	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832444	chr12:64981484-65168472	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv559203	chr12:65002969-65199922	Genic enhancers Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1045216	chr12:65009102-65176894	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv541513	chr12:65009102-65176894	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
5	nsv469457	chr12:65009243-65195977	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
6	nsv559204	chr12:65009243-65195977	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	nsv899209	chr12:65068686-65184236	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv899210	chr12:65076498-65184236	Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17100621	TBC1D30	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:65106400-65152600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:65110600-65138400	Weak transcription	Stomach Mucosa	stomach
3	chr12:65111600-65146800	Strong transcription	Fetal Intestine Large	intestine
4	chr12:65121600-65139400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr12:65124200-65138200	Strong transcription	Fetal Stomach	stomach
6	chr12:65124800-65137200	Strong transcription	Fetal Intestine Small	intestine
7	chr12:65125000-65136400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr12:65125200-65152400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr12:65125600-65144400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr12:65126800-65134200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr12:65126800-65138400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr12:65126800-65147800	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr12:65127200-65134600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr12:65127200-65134600	Strong transcription	Primary B cells from peripheral blood	blood
15	chr12:65127200-65134800	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr12:65127200-65135000	Strong transcription	Placenta	Placenta
17	chr12:65127200-65135000	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr12:65127200-65136200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr12:65127200-65138200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr12:65127200-65139600	Strong transcription	Duodenum Smooth Muscle	Duodenum
21	chr12:65127200-65140000	Strong transcription	Lung	lung
22	chr12:65127200-65141200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr12:65127200-65141600	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr12:65127200-65142200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr12:65127200-65146000	Strong transcription	Stomach Smooth Muscle	stomach
26	chr12:65127200-65146800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:65127200-65147800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr12:65127200-65149000	Strong transcription	Primary T cells from cord blood	blood
29	chr12:65127400-65134600	Strong transcription	Rectal Mucosa Donor 31	rectum
30	chr12:65127400-65135000	Strong transcription	Duodenum Mucosa	Duodenum
31	chr12:65127400-65138200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr12:65127400-65139600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr12:65127400-65142400	Strong transcription	Liver	Liver
34	chr12:65127400-65145400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr12:65127400-65148400	Strong transcription	Dnd41	blood
36	chr12:65128000-65138800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr12:65128000-65145600	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr12:65128200-65137400	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr12:65128200-65138600	Strong transcription	Adipose Nuclei	Adipose
40	chr12:65128200-65138800	Strong transcription	Brain Substantia Nigra	brain
41	chr12:65128400-65134000	Weak transcription	Psoas Muscle	Psoas
42	chr12:65128400-65134800	Strong transcription	Brain Inferior Temporal Lobe	brain
43	chr12:65128400-65140200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr12:65128400-65144800	Strong transcription	Fetal Brain Female	brain
45	chr12:65128400-65146800	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr12:65128800-65138200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr12:65129000-65136200	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr12:65129000-65138400	Strong transcription	Brain Hippocampus Middle	brain
49	chr12:65129000-65145600	Strong transcription	Fetal Muscle Trunk	muscle
50	chr12:65129200-65136400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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