Variant report

Variant	rs1317365
Chromosome Location	chr3:160278478-160278479
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	POLR2A	chr3:160275859-160280661	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160272617..160274929-chr3:160276167..160279036,2	MCF-7	breast:
2	chr3:160270076..160273601-chr3:160274357..160279300,5	MCF-7	breast:

Variant related genes	Relation type
KRT8P12	TF binding region

Extended variants
information (count: 64 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10212236	0.82[EUR][1000 genomes]
rs10513551	0.81[CEU][hapmap];0.84[GIH][hapmap]
rs13403	0.81[CEU][hapmap];0.84[GIH][hapmap]
rs1451761	0.81[CEU][hapmap];0.84[GIH][hapmap]
rs1451762	0.81[CEU][hapmap]
rs1451763	0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs1551190	0.87[GIH][hapmap]
rs17236544	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs17570467	0.85[CEU][hapmap];0.89[GIH][hapmap]
rs1882126	0.85[CEU][hapmap];0.89[GIH][hapmap]
rs1882127	0.85[CEU][hapmap];0.89[GIH][hapmap];0.81[EUR][1000 genomes]
rs1920642	0.85[CEU][hapmap]
rs1920664	0.85[CEU][hapmap]
rs2279457	0.81[CEU][hapmap];0.87[GIH][hapmap]
rs2305407	0.87[CEU][hapmap]
rs28705750	0.82[EUR][1000 genomes]
rs2886825	0.85[EUR][1000 genomes]
rs3773372	0.85[CEU][hapmap];0.89[GIH][hapmap]
rs3851364	0.85[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap]
rs3851366	0.81[CEU][hapmap];0.81[GIH][hapmap]
rs4679656	0.83[ASN][1000 genomes]
rs4679885	0.81[CEU][hapmap];0.84[GIH][hapmap]
rs4679890	0.88[CEU][hapmap];0.84[GIH][hapmap];0.81[TSI][hapmap]
rs4679891	0.84[CEU][hapmap]
rs4679897	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4679899	0.85[CEU][hapmap]
rs4680579	0.81[CEU][hapmap];0.84[GIH][hapmap]
rs4680580	0.81[CEU][hapmap];0.84[GIH][hapmap]
rs4680585	0.81[CEU][hapmap];0.87[GIH][hapmap]
rs4680588	0.81[CEU][hapmap];0.87[GIH][hapmap]
rs58322641	0.81[EUR][1000 genomes]
rs6441319	0.84[CEU][hapmap];0.84[GIH][hapmap];0.82[TSI][hapmap]
rs6441320	0.81[CEU][hapmap];0.87[GIH][hapmap]
rs6441324	0.85[CEU][hapmap]
rs6768975	0.85[CEU][hapmap];0.89[GIH][hapmap]
rs6789211	0.81[ASN][1000 genomes]
rs6798668	0.88[CEU][hapmap]
rs6801300	0.81[CEU][hapmap]
rs721022	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs721023	0.88[CEU][hapmap];0.89[GIH][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs7611130	0.81[CEU][hapmap];0.84[GIH][hapmap]
rs7618974	0.85[CEU][hapmap];0.89[GIH][hapmap]
rs7621724	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs7627749	0.81[EUR][1000 genomes]
rs7627756	0.92[CEU][hapmap];0.87[GIH][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs7629	0.81[CEU][hapmap];0.84[GIH][hapmap]
rs7629423	0.89[ASW][hapmap];0.90[CHB][hapmap];0.80[CHD][hapmap];0.95[JPT][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs7631792	0.81[CEU][hapmap];0.84[GIH][hapmap]
rs7632307	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7634108	0.83[CEU][hapmap]
rs7634826	0.81[CEU][hapmap];0.87[GIH][hapmap]
rs7640072	0.84[CEU][hapmap]
rs7643779	0.85[CEU][hapmap];0.89[GIH][hapmap]
rs7645832	0.82[EUR][1000 genomes]
rs7647873	0.85[CEU][hapmap];0.89[GIH][hapmap]
rs9862595	0.88[CEU][hapmap];0.89[GIH][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9968151	0.81[CEU][hapmap];0.84[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	esv1801767	chr3:159950498-160279411	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	nsv1008519	chr3:160038710-160292589	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	255 gene(s)	inside rSNPs	diseases
6	nsv877701	chr3:160228001-160283815	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
7	nsv877702	chr3:160262803-160304614	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1317365	IFT80	cis	parietal	SCAN
rs1317365	BCHE	cis	parietal	SCAN
rs1317365	AF038199	cis	multi-tissue	Pritchard

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160234600-160281000	Weak transcription	Aorta	Aorta
2	chr3:160240200-160280400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr3:160246600-160279200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr3:160247000-160281000	Weak transcription	Thymus	Thymus
5	chr3:160249200-160279000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr3:160251200-160282000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:160254000-160279800	Weak transcription	Placenta	Placenta
8	chr3:160254200-160278800	Weak transcription	HMEC	breast
9	chr3:160258800-160279000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr3:160260200-160279600	Weak transcription	Osteobl	bone
11	chr3:160261800-160281000	Weak transcription	Ovary	ovary
12	chr3:160264200-160282000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr3:160268400-160279200	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr3:160268400-160281000	Weak transcription	Fetal Thymus	thymus
15	chr3:160268400-160281600	Weak transcription	Fetal Stomach	stomach
16	chr3:160268800-160279800	Weak transcription	NHDF-Ad	bronchial
17	chr3:160269000-160279200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr3:160269000-160279400	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr3:160269200-160281000	Weak transcription	Fetal Intestine Large	intestine
20	chr3:160269400-160279200	Weak transcription	Dnd41	blood
21	chr3:160269400-160279200	Weak transcription	K562	blood
22	chr3:160269400-160281600	Weak transcription	Fetal Kidney	kidney
23	chr3:160269400-160281600	Weak transcription	Fetal Lung	lung
24	chr3:160269600-160278800	Weak transcription	NHEK	skin
25	chr3:160269600-160279200	Weak transcription	NH-A	brain
26	chr3:160269600-160279200	Weak transcription	NHLF	lung
27	chr3:160269800-160279200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr3:160269800-160279600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr3:160270000-160281800	Weak transcription	Fetal Muscle Trunk	muscle
30	chr3:160270200-160282000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:160270400-160280800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr3:160271200-160279200	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr3:160271400-160281000	Weak transcription	Fetal Muscle Leg	muscle
34	chr3:160272000-160279200	Weak transcription	Duodenum Mucosa	Duodenum
35	chr3:160272400-160279400	Weak transcription	Brain Hippocampus Middle	brain
36	chr3:160272400-160279800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr3:160272600-160278600	Weak transcription	A549	lung
38	chr3:160272600-160279200	Weak transcription	Stomach Mucosa	stomach
39	chr3:160272600-160280000	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr3:160272600-160281000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr3:160272800-160279600	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr3:160272800-160280200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr3:160273000-160279200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr3:160273000-160279200	Weak transcription	Primary B cells from peripheral blood	blood
45	chr3:160273000-160279400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr3:160273000-160279600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:160273000-160279600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr3:160273000-160280800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr3:160273000-160281000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr3:160273000-160281000	Weak transcription	Primary T cells fromperipheralblood	blood

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