Variant report

Variant	rs35498840
Chromosome Location	chr3:160394315-160394316
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	SP1	chr3:160394208-160395837	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160283415..160285026-chr3:160392303..160394437,2	MCF-7	breast:
2	chr3:160392640..160394500-chr3:160414229..160416051,2	MCF-7	breast:

Variant related genes	Relation type
ARL14	TF binding region
ENSG00000207084	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10460866	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10936203	0.90[CHB][hapmap]
rs11711627	0.80[ASN][1000 genomes]
rs11712392	0.82[ASN][1000 genomes]
rs11713230	0.82[ASN][1000 genomes]
rs11720693	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12639488	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs13062928	0.97[AFR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13065269	0.82[ASN][1000 genomes]
rs13072556	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13074231	0.82[ASN][1000 genomes]
rs13075424	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13085507	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1403045	0.83[CEU][hapmap]
rs16831337	0.84[CEU][hapmap]
rs17826257	0.90[CHB][hapmap]
rs1879797	0.87[CEU][hapmap]
rs1882125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1920650	0.80[ASN][1000 genomes]
rs2141668	0.80[ASN][1000 genomes]
rs2367209	0.86[EUR][1000 genomes]
rs34058107	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34444753	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35008770	0.80[ASN][1000 genomes]
rs4133253	0.84[CEU][hapmap]
rs4679903	0.80[ASN][1000 genomes]
rs4679904	0.82[ASN][1000 genomes]
rs57718211	0.99[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60339919	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6792943	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6806755	0.84[CEU][hapmap]
rs71314011	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7610939	0.84[CEU][hapmap]
rs7633839	1.00[CEU][hapmap];0.80[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7634255	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv877703	chr3:160325458-160398885	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs35498840	IFT80	cis	parietal	SCAN
rs35498840	SMC4	Cis_1M	lymphoblastoid	RTeQTL
rs35498840	KLRB1	trans	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160385200-160395000	Weak transcription	Colonic Mucosa	Colon
2	chr3:160389400-160395200	Weak transcription	Pancreas	Pancrea
3	chr3:160389400-160395400	Weak transcription	Small Intestine	intestine
4	chr3:160391400-160395200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:160392000-160394600	Enhancers	A549	lung
6	chr3:160392000-160395200	Weak transcription	HepG2	liver
7	chr3:160393200-160394800	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr3:160393400-160394600	Enhancers	Hela-S3	cervix
9	chr3:160393400-160394800	Enhancers	Duodenum Mucosa	Duodenum
10	chr3:160393400-160395000	Enhancers	Fetal Intestine Small	intestine
11	chr3:160393400-160395000	Enhancers	NHEK	skin
12	chr3:160393400-160395200	Enhancers	Fetal Intestine Large	intestine
13	chr3:160393400-160395800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr3:160393400-160395800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr3:160393400-160397000	Enhancers	HMEC	breast
16	chr3:160393400-160397200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr3:160393400-160397400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:160393600-160394600	Enhancers	Rectal Mucosa Donor 29	rectum
19	chr3:160393600-160395000	Enhancers	NH-A	brain
20	chr3:160393600-160395200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr3:160394000-160395200	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr3:160394200-160394400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:160394200-160394400	Flanking Active TSS	Stomach Mucosa	stomach
24	chr3:160394200-160397400	Enhancers	ES-I3 Cell Line	embryonic stem cell

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