Variant report

Variant	rs10475468
Chromosome Location	chr5:9538757-9538758
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	chr5:9534301..9536161-chr5:9536670..9538887,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs11958932	0.91[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs3777370	0.84[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3777371	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3798087	0.89[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs3798089	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3798090	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs3798092	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs422309	0.91[AFR][1000 genomes]
rs432989	0.83[AFR][1000 genomes]
rs456885	0.80[AFR][1000 genomes]
rs460234	0.91[AFR][1000 genomes]
rs461337	0.82[AFR][1000 genomes]
rs461750	0.85[AFR][1000 genomes]
rs464621	0.82[AFR][1000 genomes]
rs4702633	0.91[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs605126	0.94[AFR][1000 genomes]
rs6881628	0.89[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6882326	0.89[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs7703528	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881438	chr5:8728874-9695667	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1015378	chr5:9053542-9617963	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv537640	chr5:9053542-9617963	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
4	nsv597071	chr5:9182376-9760599	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1032672	chr5:9182409-9843893	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1035075	chr5:9182584-9843723	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv537641	chr5:9182584-9843723	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv1034637	chr5:9182784-9741743	Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv537642	chr5:9182784-9741743	Enhancers Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv1028656	chr5:9196001-9837040	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv1016885	chr5:9218932-9575594	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv1026078	chr5:9222811-9591290	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv1022137	chr5:9225121-9745434	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	nsv537643	chr5:9225121-9745434	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv1022574	chr5:9314645-9647238	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	nsv869120	chr5:9491731-10149255	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
17	nsv1018275	chr5:9504897-9560199	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	nsv537644	chr5:9504897-9560199	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
19	nsv597073	chr5:9533854-9550642	Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10475468	CTD-2001E22.2	cis	Adipose Subcutaneous	GTEx
rs10475468	CTD-2001E22.2	cis	lung	GTEx
rs10475468	CTD-2001E22.2	cis	Muscle Skeletal	GTEx
rs10475468	CTD-2001E22.2	cis	Nerve Tibial	GTEx
rs10475468	CTD-2001E22.2	cis	Esophagus Muscularis	GTEx

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:9521200-9544400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:9525400-9542000	Weak transcription	Small Intestine	intestine
3	chr5:9528400-9544200	Weak transcription	Fetal Intestine Small	intestine
4	chr5:9529600-9544400	Weak transcription	Pancreas	Pancrea
5	chr5:9529600-9544800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr5:9530200-9543600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr5:9530200-9544600	Weak transcription	Lung	lung
8	chr5:9530400-9544200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr5:9530400-9544800	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr5:9533400-9543600	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr5:9534200-9540200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr5:9534200-9543200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr5:9534400-9540600	Weak transcription	Osteobl	bone
14	chr5:9534400-9542800	Weak transcription	Fetal Kidney	kidney
15	chr5:9534400-9542800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr5:9534600-9538800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr5:9534600-9543000	Weak transcription	Brain Germinal Matrix	brain
18	chr5:9534800-9538800	Enhancers	Fetal Heart	heart
19	chr5:9534800-9543000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr5:9535200-9540200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr5:9535400-9540800	Weak transcription	NH-A	brain
22	chr5:9535400-9543000	Weak transcription	Aorta	Aorta
23	chr5:9535800-9538800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr5:9535800-9544000	Weak transcription	Fetal Stomach	stomach
25	chr5:9536000-9538800	Weak transcription	NHLF	lung
26	chr5:9536000-9542400	Enhancers	Breast Myoepithelial Primary Cells	Breast
27	chr5:9536200-9538800	Weak transcription	Brain Angular Gyrus	brain
28	chr5:9536200-9538800	Weak transcription	Brain Anterior Caudate	brain
29	chr5:9536200-9539200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr5:9536200-9540200	Weak transcription	Brain Hippocampus Middle	brain
31	chr5:9536200-9542800	Weak transcription	HMEC	breast
32	chr5:9536200-9543200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr5:9537200-9540200	Weak transcription	Fetal Muscle Trunk	muscle
34	chr5:9537200-9540600	Weak transcription	Fetal Muscle Leg	muscle
35	chr5:9537400-9544200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr5:9537600-9543000	Weak transcription	Fetal Lung	lung
37	chr5:9538000-9538800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr5:9538000-9542800	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr5:9538000-9544400	Weak transcription	Liver	Liver
40	chr5:9538200-9540200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr5:9538200-9540600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr5:9538200-9540800	Weak transcription	Brain Substantia Nigra	brain
43	chr5:9538200-9541000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr5:9538200-9541000	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr5:9538400-9539200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr5:9538400-9539400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr5:9538400-9539400	Enhancers	Colon Smooth Muscle	Colon
48	chr5:9538600-9538800	Enhancers	Brain Cingulate Gyrus	brain
49	chr5:9538600-9538800	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr5:9538600-9538800	Enhancers	NHDF-Ad	bronchial

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