Variant report

Variant	rs7627555
Chromosome Location	chr3:160034574-160034575
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160031130..160033296-chr3:160034351..160037164,2	K562	blood:

Extended variants
information (count: 65 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1047210	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10513551	0.85[CEU][hapmap]
rs10923	0.82[JPT][hapmap]
rs10936201	0.82[JPT][hapmap]
rs11706810	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11708118	0.82[JPT][hapmap]
rs11709336	0.82[JPT][hapmap]
rs11718121	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11719750	0.82[JPT][hapmap]
rs11720689	0.82[JPT][hapmap]
rs12632030	0.86[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13403	0.85[CEU][hapmap]
rs1451760	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1451761	0.85[CEU][hapmap]
rs1451762	0.85[CEU][hapmap]
rs17236473	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17826221	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1873076	0.81[JPT][hapmap]
rs1953506	0.85[CEU][hapmap]
rs2279457	0.85[CEU][hapmap]
rs2305407	0.87[CEU][hapmap];0.83[JPT][hapmap]
rs3732706	0.92[CEU][hapmap];0.93[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap]
rs3773372	0.81[CEU][hapmap]
rs3851365	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.95[MEX][hapmap];0.80[MKK][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3851366	0.85[CEU][hapmap]
rs4679881	0.85[CEU][hapmap];0.83[JPT][hapmap]
rs4679885	0.85[CEU][hapmap]
rs4680576	0.85[CEU][hapmap]
rs4680579	0.85[CEU][hapmap]
rs4680580	0.85[CEU][hapmap]
rs4680585	0.85[CEU][hapmap]
rs4680588	0.85[CEU][hapmap]
rs4680591	0.81[EUR][1000 genomes]
rs55992947	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6441313	0.85[CEU][hapmap]
rs6441314	0.85[CEU][hapmap]
rs6441319	0.81[CEU][hapmap]
rs6441320	0.85[CEU][hapmap]
rs6785881	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6790951	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6791056	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6791261	0.85[CEU][hapmap];0.83[JPT][hapmap]
rs6793560	0.88[CEU][hapmap]
rs6798183	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6798668	0.81[CEU][hapmap]
rs6803828	0.85[CEU][hapmap]
rs6809153	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7355951	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7611130	0.85[CEU][hapmap]
rs7620828	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7624902	0.85[CEU][hapmap]
rs7627756	0.81[CEU][hapmap]
rs7629	0.85[CEU][hapmap]
rs7631792	0.85[CEU][hapmap]
rs7634108	0.84[CEU][hapmap]
rs7634826	0.85[CEU][hapmap]
rs869467	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs869468	0.85[CEU][hapmap]
rs9968151	0.85[CEU][hapmap]

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	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	esv1800136	chr3:159950498-160278160	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	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
6	esv1801474	chr3:160012843-160153305	Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	206 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7627555	IFT80	cis	parietal	SCAN
rs7627555	SMC4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159971400-160035800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:159974200-160038000	Weak transcription	Fetal Brain Male	brain
3	chr3:159975200-160036000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr3:159975600-160046600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr3:159976200-160039000	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:159977800-160073000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr3:159981200-160038200	Weak transcription	Esophagus	oesophagus
8	chr3:159984800-160038200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr3:159992400-160035400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr3:159992800-160036400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr3:159992800-160036600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr3:159996400-160037000	Weak transcription	Primary B cells from cord blood	blood
13	chr3:159996600-160038400	Weak transcription	Brain Hippocampus Middle	brain
14	chr3:159997200-160037200	Weak transcription	Brain Angular Gyrus	brain
15	chr3:159997200-160046600	Weak transcription	Fetal Lung	lung
16	chr3:159997600-160035600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr3:159999800-160035400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:159999800-160047800	Weak transcription	Lung	lung
19	chr3:160010000-160047800	Weak transcription	HepG2	liver
20	chr3:160010000-160048600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr3:160010000-160048800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:160014600-160039400	Weak transcription	GM12878-XiMat	blood
23	chr3:160014800-160037200	Weak transcription	Colon Smooth Muscle	Colon
24	chr3:160014800-160039600	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr3:160015000-160038200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr3:160015000-160044000	Weak transcription	Osteobl	bone
27	chr3:160015400-160048400	Weak transcription	A549	lung
28	chr3:160015800-160048800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:160018000-160048600	Weak transcription	HSMM	muscle
30	chr3:160020600-160037600	Weak transcription	NH-A	brain
31	chr3:160021200-160043400	Weak transcription	NHDF-Ad	bronchial
32	chr3:160022400-160038800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr3:160023000-160036800	Weak transcription	Stomach Smooth Muscle	stomach
34	chr3:160023200-160037800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr3:160024200-160035600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr3:160024400-160043400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:160025400-160038800	Weak transcription	Liver	Liver
38	chr3:160025400-160056000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:160025400-160073000	Weak transcription	Fetal Muscle Trunk	muscle
40	chr3:160025600-160035200	Weak transcription	Dnd41	blood
41	chr3:160025600-160036200	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr3:160025600-160048400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr3:160025600-160048600	Weak transcription	Brain Substantia Nigra	brain
44	chr3:160025600-160072000	Weak transcription	Thymus	Thymus
45	chr3:160025600-160073200	Weak transcription	Left Ventricle	heart
46	chr3:160026200-160035600	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr3:160026200-160047600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:160026600-160036400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr3:160027200-160036400	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr3:160027800-160036000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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