Variant report

Variant	rs1341987
Chromosome Location	chr1:223309213-223309214
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	STAT3	chr1:223307101-223309223	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:223308071..223311101-chr1:223314181..223317156,4	K562	blood:

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

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1640827	0.82[CEU][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17661703	0.81[ASN][1000 genomes]
rs1773756	0.81[ASN][1000 genomes]
rs1773757	0.81[ASN][1000 genomes]
rs2096141	0.94[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2096142	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]
rs2247421	0.92[CHD][hapmap];0.81[JPT][hapmap];0.81[MKK][hapmap];0.82[YRI][hapmap]
rs2353475	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2353476	0.88[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2353477	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2883182	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs34849527	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs35442320	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs5744105	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs5744113	0.94[ASW][hapmap];0.85[CEU][hapmap];0.87[CHB][hapmap];0.94[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5744129	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs723960	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs851171	0.92[CHD][hapmap];0.81[JPT][hapmap]
rs851178	0.89[JPT][hapmap]
rs851180	0.89[JPT][hapmap];0.83[MEX][hapmap]
rs851186	0.89[JPT][hapmap]
rs851191	0.82[CEU][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9442047	0.88[ASW][hapmap];0.94[CHD][hapmap];0.81[JPT][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];0.98[MKK][hapmap];0.84[TSI][hapmap];0.82[YRI][hapmap];0.81[ASN][1000 genomes]
rs9442048	0.81[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
rs1341987	SUSD4	cis	parietal	SCAN
rs1341987	TLR5	cis	cerebellum	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223303200-223314600	Weak transcription	Spleen	Spleen
2	chr1:223306600-223310000	Enhancers	Lung	lung
3	chr1:223306800-223310000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:223306800-223310600	Enhancers	Esophagus	oesophagus
5	chr1:223307600-223311400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:223307600-223311600	Enhancers	Adipose Nuclei	Adipose
7	chr1:223307600-223311600	Enhancers	Placenta	Placenta
8	chr1:223307600-223314200	Weak transcription	Right Ventricle	heart
9	chr1:223307600-223315800	Weak transcription	Right Atrium	heart
10	chr1:223307800-223309400	Enhancers	Muscle Satellite Cultured Cells	--
11	chr1:223307800-223309400	Bivalent Enhancer	Brain Hippocampus Middle	brain
12	chr1:223307800-223309400	Enhancers	Duodenum Smooth Muscle	Duodenum
13	chr1:223307800-223309600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:223307800-223309800	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr1:223307800-223309800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:223307800-223309800	Enhancers	Rectal Smooth Muscle	rectum
17	chr1:223307800-223310400	Weak transcription	Liver	Liver
18	chr1:223307800-223310400	Weak transcription	Brain Anterior Caudate	brain
19	chr1:223307800-223310400	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr1:223307800-223310400	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr1:223307800-223311200	Enhancers	HMEC	breast
22	chr1:223307800-223312600	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr1:223308000-223309600	Enhancers	H1 Cell Line	embryonic stem cell
24	chr1:223308000-223311000	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr1:223308200-223309400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:223308200-223309600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
27	chr1:223308200-223309800	Enhancers	Fetal Muscle Trunk	muscle
28	chr1:223308400-223310600	Enhancers	Psoas Muscle	Psoas
29	chr1:223308600-223309600	Bivalent Enhancer	Fetal Stomach	stomach
30	chr1:223308600-223309800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:223308600-223309800	Enhancers	Fetal Muscle Leg	muscle
32	chr1:223308600-223309800	Genic enhancers	Monocytes-CD14+_RO01746	blood
33	chr1:223308600-223314000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr1:223308800-223309400	Enhancers	Primary B cells from cord blood	blood
35	chr1:223308800-223309400	Enhancers	NHLF	lung
36	chr1:223308800-223309600	Enhancers	Colon Smooth Muscle	Colon
37	chr1:223308800-223309600	Enhancers	Stomach Smooth Muscle	stomach
38	chr1:223308800-223310600	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
39	chr1:223308800-223310800	Weak transcription	Hela-S3	cervix
40	chr1:223308800-223314000	Weak transcription	Gastric	stomach
41	chr1:223308800-223314000	Weak transcription	Pancreas	Pancrea
42	chr1:223308800-223314000	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr1:223308800-223314400	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr1:223308800-223314600	Weak transcription	Colonic Mucosa	Colon
45	chr1:223309000-223309400	Weak transcription	Ovary	ovary
46	chr1:223309000-223309800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:223309000-223309800	Enhancers	Osteobl	bone
48	chr1:223309000-223310400	Weak transcription	NHDF-Ad	bronchial
49	chr1:223309000-223310600	Weak transcription	Duodenum Mucosa	Duodenum
50	chr1:223309000-223310600	Weak transcription	HSMM	muscle

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