Variant report

Variant	rs2096142
Chromosome Location	chr1:223311845-223311846
allele	A/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	RFX5	chr1:223311833-223311847	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:223311533..223314395-chr1:223314636..223318058,5	K562	blood:
2	chr1:223295440..223297086-chr1:223310909..223313590,2	MCF-7	breast:

Variant related genes	Relation type
TLR5	TF binding region
ENSG00000236846	Chromatin interaction
ENSG00000187554	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1341987	0.88[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1640827	0.85[CEU][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17661703	0.85[ASN][1000 genomes]
rs1773755	0.86[ASN][1000 genomes]
rs1773756	0.85[ASN][1000 genomes]
rs1773757	0.85[ASN][1000 genomes]
rs1773758	0.86[ASN][1000 genomes]
rs2096141	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2247421	0.81[CHB][hapmap];0.97[CHD][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs2353475	0.90[ASN][1000 genomes]
rs2353476	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2353477	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2883182	0.90[ASN][1000 genomes]
rs34849527	0.90[ASN][1000 genomes]
rs35442320	0.90[ASN][1000 genomes]
rs35511158	0.86[ASN][1000 genomes]
rs5744105	0.91[ASN][1000 genomes]
rs5744113	0.82[ASW][hapmap];0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.81[JPT][hapmap];0.82[LWK][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5744129	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61837568	0.83[ASN][1000 genomes]
rs61837569	0.83[ASN][1000 genomes]
rs61837573	0.83[ASN][1000 genomes]
rs61837574	0.83[ASN][1000 genomes]
rs61837575	0.83[ASN][1000 genomes]
rs61837577	0.82[ASN][1000 genomes]
rs723960	0.90[ASN][1000 genomes]
rs72743865	0.83[ASN][1000 genomes]
rs851166	0.84[ASN][1000 genomes]
rs851171	0.97[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs851178	0.89[JPT][hapmap]
rs851180	0.89[JPT][hapmap]
rs851186	0.89[JPT][hapmap]
rs851191	0.85[CEU][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9442047	0.81[CHB][hapmap];1.00[CHD][hapmap];0.81[JPT][hapmap];0.83[MEX][hapmap];0.84[TSI][hapmap];0.87[ASN][1000 genomes]
rs9442048	0.87[ASN][1000 genomes]
rs975089	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1014896	chr1:223070446-223327185	Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv832659	chr1:223294767-223438487	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2096142	TLR5	cis	cerebellum	SCAN
rs2096142	SUSD4	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223303200-223314600	Weak transcription	Spleen	Spleen
2	chr1:223307600-223314200	Weak transcription	Right Ventricle	heart
3	chr1:223307600-223315800	Weak transcription	Right Atrium	heart
4	chr1:223307800-223312600	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr1:223308600-223314000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:223308800-223314000	Weak transcription	Gastric	stomach
7	chr1:223308800-223314000	Weak transcription	Pancreas	Pancrea
8	chr1:223308800-223314000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr1:223308800-223314400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr1:223308800-223314600	Weak transcription	Colonic Mucosa	Colon
11	chr1:223309000-223314200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:223309200-223315800	Weak transcription	Primary T cells from cord blood	blood
13	chr1:223309400-223316000	Weak transcription	NHLF	lung
14	chr1:223309600-223314600	Weak transcription	Ovary	ovary
15	chr1:223309600-223314600	Weak transcription	Stomach Smooth Muscle	stomach
16	chr1:223309800-223313000	Weak transcription	Fetal Muscle Leg	muscle
17	chr1:223309800-223313600	Weak transcription	Fetal Muscle Trunk	muscle
18	chr1:223309800-223314000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr1:223309800-223315600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr1:223310200-223316000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr1:223310600-223314000	Weak transcription	Esophagus	oesophagus
22	chr1:223310600-223314000	Weak transcription	Psoas Muscle	Psoas
23	chr1:223310600-223314200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr1:223310600-223315400	Weak transcription	Lung	lung
25	chr1:223311000-223314200	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr1:223311200-223314000	Weak transcription	Duodenum Mucosa	Duodenum
27	chr1:223311200-223314000	Weak transcription	NHDF-Ad	bronchial
28	chr1:223311200-223314200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr1:223311200-223314200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:223311200-223314400	Weak transcription	HMEC	breast
31	chr1:223311200-223314400	Weak transcription	NHEK	skin
32	chr1:223311200-223314600	Weak transcription	Stomach Mucosa	stomach
33	chr1:223311200-223315800	Weak transcription	Hela-S3	cervix
34	chr1:223311200-223316000	Weak transcription	Liver	Liver
35	chr1:223311400-223314200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:223311400-223314200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:223311400-223316000	Weak transcription	Fetal Intestine Large	intestine
38	chr1:223311600-223312600	Enhancers	Monocytes-CD14+_RO01746	blood
39	chr1:223311600-223313000	Enhancers	Primary neutrophils fromperipheralblood	blood
40	chr1:223311600-223313800	Weak transcription	Placenta	Placenta
41	chr1:223311600-223313800	Weak transcription	Fetal Thymus	thymus
42	chr1:223311600-223314000	Weak transcription	Adipose Nuclei	Adipose
43	chr1:223311600-223314000	Weak transcription	Brain Anterior Caudate	brain
44	chr1:223311600-223314000	Weak transcription	Fetal Lung	lung
45	chr1:223311600-223314200	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr1:223311600-223315600	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr1:223311600-223316000	Weak transcription	Fetal Intestine Small	intestine
48	chr1:223311600-223316200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr1:223311800-223312200	Enhancers	Primary B cells from cord blood	blood

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