Variant report

Variant	rs11070411
Chromosome Location	chr15:44058634-44058635
allele	C/G
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	chr15:44058627-44059022	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:44054982..44059641-chr15:44059790..44066522,8	MCF-7	breast:
2	chr15:44056557..44058823-chr15:44066923..44069715,2	K562	blood:
3	chr15:44052411..44054206-chr15:44056852..44059319,2	MCF-7	breast:
4	chr15:44057941..44060272-chr15:44063922..44065523,2	K562	blood:

Variant related genes	Relation type
PDIA3	TF binding region
ENSG00000167004	Chromatin interaction
ENSG00000128886	Chromatin interaction
ENSG00000140264	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10163069	1.00[CEU][hapmap];0.84[GIH][hapmap];0.84[LWK][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12443084	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs17727853	1.00[CEU][hapmap]
rs17795279	1.00[CEU][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs2412821	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2729494	1.00[CEU][hapmap];0.96[YRI][hapmap];0.89[EUR][1000 genomes]
rs28410121	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2918943	0.96[YRI][hapmap]
rs2918947	0.83[EUR][1000 genomes]
rs2930529	0.93[EUR][1000 genomes]
rs2930530	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2930531	1.00[CEU][hapmap];0.96[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3102448	0.88[EUR][1000 genomes]
rs3110081	0.86[EUR][1000 genomes]
rs35822148	0.87[EUR][1000 genomes]
rs3862143	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3986209	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4644832	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4923964	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4923965	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs495880	0.94[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.89[EUR][1000 genomes]
rs514311	0.94[CEU][hapmap];0.95[YRI][hapmap];0.84[EUR][1000 genomes]
rs528764	1.00[CEU][hapmap];0.95[YRI][hapmap];0.89[EUR][1000 genomes]
rs541871	0.94[CEU][hapmap];0.96[YRI][hapmap];0.84[EUR][1000 genomes]
rs62018940	0.93[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs62018944	0.88[EUR][1000 genomes]
rs6493090	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs654276	0.94[CEU][hapmap];0.83[GIH][hapmap];0.85[MEX][hapmap];0.83[YRI][hapmap];0.89[EUR][1000 genomes]
rs678084	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7174241	0.84[GIH][hapmap]
rs7174260	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7178230	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8030536	1.00[CEU][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs8038068	1.00[CEU][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1846172	chr15:43632138-44116986	Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1846701	chr15:43759774-44116986	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	esv2758379	chr15:43823158-44148641	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
4	esv2760028	chr15:43823158-44148641	Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
5	nsv427960	chr15:43823158-44148641	Flanking Active TSS Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
6	esv2757598	chr15:43831923-44058634	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats 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	31 gene(s)	inside rSNPs	diseases
7	nsv1037786	chr15:43888926-44318587	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
8	nsv542370	chr15:43888926-44318587	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
9	nsv431387	chr15:43929378-44862930	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
10	nsv931051	chr15:43988761-44833518	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	154 gene(s)	inside rSNPs	diseases
11	esv33661	chr15:44016519-44064420	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
12	nsv1036318	chr15:44053617-44160773	Flanking Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs11070411	C15orf63	cis	brain	seeQTL
rs11070411	ZSCAN29	cis	multi-tissue	Pritchard
rs11070411	WDR76	cis	parietal	SCAN
rs11070411	ZNF690	cis	multi-tissue	Pritchard
rs11070411	TUBGCP4	cis	parietal	SCAN
rs11070411	MAPKBP1	cis	parietal	SCAN
rs11070411	ZSCAN29	cis	brain	seeQTL
rs11070411	ZSCAN29	cis	lymphoblastoid	seeQTL
rs11070411	STRC	cis	multi-tissue	Pritchard
rs11070411	TGM5	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44040200-44062000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:44041000-44068800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:44042000-44066600	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr15:44042000-44066800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
5	chr15:44042000-44067000	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr15:44042200-44067000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
7	chr15:44042600-44066600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
8	chr15:44043000-44066800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr15:44043400-44063200	Strong transcription	Monocytes-CD14+_RO01746	blood
10	chr15:44043400-44066600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr15:44043400-44066600	Strong transcription	Fetal Thymus	thymus
12	chr15:44043400-44066800	Strong transcription	HUES6 Cell Line	embryonic stem cell
13	chr15:44043400-44066800	Strong transcription	Placenta	Placenta
14	chr15:44043400-44067000	Strong transcription	Osteobl	bone
15	chr15:44043400-44067200	Strong transcription	HSMM	muscle
16	chr15:44043600-44063000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr15:44043600-44063800	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr15:44043600-44066600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr15:44043600-44066800	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr15:44043800-44066800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr15:44044000-44063800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr15:44044000-44063800	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr15:44044000-44066600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr15:44044000-44067000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr15:44044400-44065600	Strong transcription	HUVEC	blood vessel
26	chr15:44044400-44066600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr15:44044400-44068200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr15:44044600-44065600	Strong transcription	Brain Anterior Caudate	brain
29	chr15:44044600-44066400	Strong transcription	Adipose Nuclei	Adipose
30	chr15:44044600-44067000	Strong transcription	Fetal Intestine Large	intestine
31	chr15:44044800-44063800	Strong transcription	Duodenum Mucosa	Duodenum
32	chr15:44044800-44065600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr15:44044800-44065600	Strong transcription	Dnd41	blood
34	chr15:44044800-44066600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr15:44045000-44065800	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr15:44045000-44067000	Strong transcription	Fetal Muscle Trunk	muscle
37	chr15:44045000-44067200	Strong transcription	Fetal Stomach	stomach
38	chr15:44045200-44066400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr15:44045200-44066600	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr15:44045200-44066800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr15:44045200-44067200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr15:44045600-44065200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr15:44045600-44065800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr15:44045600-44066600	Strong transcription	Liver	Liver
45	chr15:44045800-44065800	Strong transcription	Left Ventricle	heart
46	chr15:44045800-44065800	Strong transcription	Thymus	Thymus
47	chr15:44045800-44066400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr15:44046000-44064400	Strong transcription	Colonic Mucosa	Colon
49	chr15:44046000-44065400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr15:44046000-44068000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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