Variant report

Variant	rs39614
Chromosome Location	chr5:154199368-154199369
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:154192681..154195984-chr5:154196511..154199609,4	K562	blood:
2	chr5:154134880..154137137-chr5:154198526..154200229,3	K562	blood:
3	chr5:154197564..154200404-chr5:154207941..154209684,2	MCF-7	breast:
4	chr5:154198864..154200743-chr5:154269155..154270734,2	K562	blood:
5	chr5:154133909..154135930-chr5:154197184..154199764,3	MCF-7	breast:
6	chr5:154133441..154135046-chr5:154198681..154200668,2	MCF-7	breast:
7	chr5:154193302..154196557-chr5:154196665..154201027,5	MCF-7	breast:
8	chr5:154198123..154199805-chr5:154316637..154318536,2	K562	blood:
9	chr5:154192019..154194234-chr5:154197366..154200161,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GEMIN5-1	chr5:154198054-154199628	NONHSAT104714

No data

Variant related genes	Relation type
ENSG00000082516	Chromatin interaction
ENSG00000155506	Chromatin interaction
ENSG00000263361	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs1035368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10515727	1.00[TSI][hapmap]
rs11167705	0.82[ASN][1000 genomes]
rs12187921	1.00[CHB][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap]
rs12188498	1.00[TSI][hapmap]
rs12188828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12300	0.86[ASW][hapmap];0.87[CEU][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.85[LWK][hapmap];0.92[MKK][hapmap];0.90[TSI][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1421815	1.00[TSI][hapmap]
rs1421819	1.00[TSI][hapmap]
rs164195	0.83[EUR][1000 genomes]
rs17096232	1.00[TSI][hapmap]
rs17116409	1.00[TSI][hapmap]
rs17116411	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17116414	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17116417	1.00[TSI][hapmap]
rs17116421	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17116433	1.00[CHB][hapmap]
rs17116442	1.00[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];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17116534	0.93[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs180846	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs186971	0.86[EUR][1000 genomes]
rs1974776	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1974777	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2042168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2112223	1.00[CEU][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.91[EUR][1000 genomes]
rs2161128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2258437	0.93[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.89[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2396999	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs2431184	0.90[ASN][1000 genomes]
rs2544859	0.93[CEU][hapmap];0.89[YRI][hapmap];0.86[EUR][1000 genomes]
rs2544860	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2544866	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2544874	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2544875	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2544876	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2544880	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2544884	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs255529	0.84[ASN][1000 genomes]
rs2560063	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2644743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2644744	0.93[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.85[LWK][hapmap];0.89[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[EUR][1000 genomes]
rs2644746	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2688186	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2688187	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2688188	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2688189	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2688190	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2688191	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2688193	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2688194	0.83[EUR][1000 genomes]
rs2688195	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2688198	0.93[ASW][hapmap];1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2688199	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2688200	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2688201	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2688206	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2688208	1.00[CEU][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs32427	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs348739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs348748	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs348749	0.86[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs348750	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs348751	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs348752	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs348754	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3776984	1.00[TSI][hapmap]
rs4354100	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs454161	0.90[ASN][1000 genomes]
rs4958771	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55770418	0.90[EUR][1000 genomes]
rs56374414	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58415346	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59525998	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59749917	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6580122	0.81[ASN][1000 genomes]
rs6865950	1.00[TSI][hapmap]
rs6879277	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6884416	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6895741	1.00[TSI][hapmap]
rs702742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73276742	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73280705	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7716019	1.00[TSI][hapmap]
rs7723269	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7728194	0.86[EUR][1000 genomes]
rs816717	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs816718	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs816720	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs816722	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs816734	0.86[ASN][1000 genomes]
rs816743	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs816747	0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs888694	0.83[EUR][1000 genomes]
rs960499	0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9942412	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830521	chr5:154147567-154244266	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs39614	ANXA6	cis	parietal	SCAN
rs39614	EBF1	cis	parietal	SCAN
rs39614	CCDC69	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154167000-154203000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:154169200-154204200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
3	chr5:154169200-154204200	Strong transcription	Dnd41	blood
4	chr5:154169400-154199400	Strong transcription	Fetal Muscle Trunk	muscle
5	chr5:154169400-154200000	Strong transcription	HUES64 Cell Line	embryonic stem cell
6	chr5:154169400-154200800	Strong transcription	H1 Cell Line	embryonic stem cell
7	chr5:154169400-154201400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr5:154169400-154204000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:154169400-154204200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr5:154169400-154204200	Strong transcription	Duodenum Mucosa	Duodenum
11	chr5:154169400-154205800	Strong transcription	Skeletal Muscle Female	skeletal muscle
12	chr5:154169600-154199400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr5:154169600-154200000	Strong transcription	Fetal Muscle Leg	muscle
14	chr5:154169600-154202400	Strong transcription	Rectal Mucosa Donor 31	rectum
15	chr5:154169600-154204200	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr5:154170800-154201200	Strong transcription	Muscle Satellite Cultured Cells	--
17	chr5:154171000-154201000	Strong transcription	HSMM	muscle
18	chr5:154174000-154212200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr5:154174800-154204400	Strong transcription	Placenta	Placenta
20	chr5:154175200-154204400	Strong transcription	Osteobl	bone
21	chr5:154175200-154204600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr5:154177200-154202200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr5:154178200-154204000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr5:154181000-154201000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr5:154181000-154211600	Strong transcription	Brain Hippocampus Middle	brain
26	chr5:154181200-154204800	Strong transcription	Brain Cingulate Gyrus	brain
27	chr5:154181400-154199800	Strong transcription	Brain Inferior Temporal Lobe	brain
28	chr5:154182000-154211400	Strong transcription	Left Ventricle	heart
29	chr5:154187000-154211400	Strong transcription	Fetal Stomach	stomach
30	chr5:154187600-154204200	Strong transcription	Skeletal Muscle Male	skeletal muscle
31	chr5:154187600-154204400	Strong transcription	Brain Germinal Matrix	brain
32	chr5:154188600-154202400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr5:154189400-154206000	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr5:154189600-154200200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr5:154189800-154204600	Strong transcription	Lung	lung
36	chr5:154190000-154201200	Strong transcription	NHEK	skin
37	chr5:154190200-154200200	Strong transcription	GM12878-XiMat	blood
38	chr5:154190400-154204200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr5:154190600-154200800	Strong transcription	NHLF	lung
40	chr5:154190800-154201000	Strong transcription	Esophagus	oesophagus
41	chr5:154190800-154201200	Strong transcription	Gastric	stomach
42	chr5:154191000-154201200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr5:154191400-154201400	Strong transcription	Spleen	Spleen
44	chr5:154191600-154208600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr5:154191800-154200400	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr5:154191800-154200600	Weak transcription	Fetal Heart	heart
47	chr5:154191800-154206200	Strong transcription	Brain Anterior Caudate	brain
48	chr5:154191800-154211600	Strong transcription	Adipose Nuclei	Adipose
49	chr5:154192200-154199600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr5:154192400-154204200	Strong transcription	Brain Substantia Nigra	brain

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