Variant report

Variant	rs3203960
Chromosome Location	chr5:167891830-167891831
allele	C/T
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	chr5:167891760-167892172	A549	lung:	n/a	n/a
2	POLR2A	chr5:167891517-167891867	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr5:167891820-167892068	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
WWC1	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10038727	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10040267	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10040284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11743260	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13158266	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13158279	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13173439	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13184909	0.83[EUR][1000 genomes]
rs13185713	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13189009	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13359192	0.85[EUR][1000 genomes]
rs2085449	0.86[LWK][hapmap];0.82[TSI][hapmap];0.93[YRI][hapmap];0.83[EUR][1000 genomes]
rs2337211	0.83[EUR][1000 genomes]
rs2337212	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2337219	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs244891	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2878915	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29001621	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34197361	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34468271	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34565033	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34966676	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35030651	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs36015366	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4576167	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4976556	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4976557	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4976611	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4976612	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56168499	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62384143	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6886345	0.85[CEU][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs71603863	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7720379	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7737861	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs888773	0.85[CEU][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534607	chr5:167661667-168454396	Active TSS Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv949154	chr5:167691208-168323234	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv1023985	chr5:167756193-168285807	Strong transcription Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv537941	chr5:167756193-168285807	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	esv3444818	chr5:167770667-167902204	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv970006	chr5:167870237-167924444	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3203960	FBLL1	cis	Artery Tibial	GTEx

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:167812600-167896400	Weak transcription	Colonic Mucosa	Colon
2	chr5:167829000-167896800	Weak transcription	Stomach Mucosa	stomach
3	chr5:167837000-167896800	Weak transcription	Brain Hippocampus Middle	brain
4	chr5:167850800-167895600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr5:167852200-167900400	Strong transcription	Liver	Liver
6	chr5:167862000-167897000	Weak transcription	Brain Substantia Nigra	brain
7	chr5:167863800-167899600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr5:167864400-167897600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr5:167869800-167895600	Weak transcription	NH-A	brain
10	chr5:167874600-167899600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:167875000-167896800	Weak transcription	Fetal Lung	lung
12	chr5:167876400-167902200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr5:167877400-167895600	Weak transcription	Osteobl	bone
14	chr5:167877600-167896800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr5:167877800-167894600	Weak transcription	Fetal Brain Male	brain
16	chr5:167878200-167897200	Strong transcription	Fetal Intestine Large	intestine
17	chr5:167878400-167898000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr5:167879000-167897400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr5:167879600-167897200	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr5:167880200-167896200	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr5:167880200-167900000	Strong transcription	Duodenum Mucosa	Duodenum
22	chr5:167880400-167893000	Strong transcription	Brain Anterior Caudate	brain
23	chr5:167880400-167898200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr5:167880800-167897400	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr5:167881000-167896600	Strong transcription	Fetal Brain Female	brain
26	chr5:167881200-167901800	Strong transcription	Placenta	Placenta
27	chr5:167881800-167893200	Strong transcription	NHEK	skin
28	chr5:167884200-167893600	Strong transcription	Pancreas	Pancrea
29	chr5:167884200-167895200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr5:167884800-167901400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr5:167885000-167903000	Strong transcription	A549	lung
32	chr5:167885200-167900400	Strong transcription	Fetal Intestine Small	intestine
33	chr5:167885200-167902400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr5:167885400-167895600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr5:167885600-167893000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr5:167885600-167896800	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr5:167885600-167900800	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr5:167885800-167892000	Weak transcription	Brain Cingulate Gyrus	brain
39	chr5:167885800-167898600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr5:167885800-167912800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr5:167886000-167901000	Weak transcription	Fetal Kidney	kidney
42	chr5:167886200-167893600	Strong transcription	Fetal Stomach	stomach
43	chr5:167887200-167900400	Strong transcription	Gastric	stomach
44	chr5:167887400-167901400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr5:167887800-167893200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr5:167887800-167895000	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr5:167888000-167892400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr5:167888800-167892000	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr5:167889000-167892400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr5:167889200-167893800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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