Variant report

Variant	rs17116421
Chromosome Location	chr5:154154018-154154019
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:154134948..154137800-chr5:154152805..154155908,3	MCF-7	breast:
2	chr5:154153749..154156019-chr5:154157510..154160380,3	MCF-7	breast:
3	chr5:154132476..154143251-chr5:154145354..154162500,38	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155506	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs1035368	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10515727	1.00[TSI][hapmap]
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];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12300	0.80[ASW][hapmap];0.87[CEU][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.88[LWK][hapmap];0.96[MKK][hapmap];0.90[TSI][hapmap];0.85[YRI][hapmap];0.84[EUR][1000 genomes]
rs1421815	1.00[TSI][hapmap]
rs1421819	1.00[TSI][hapmap]
rs17096232	1.00[TSI][hapmap]
rs17116409	1.00[TSI][hapmap]
rs17116411	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17116414	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17116417	1.00[TSI][hapmap]
rs17116433	1.00[CHB][hapmap]
rs17116442	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17116534	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.85[EUR][1000 genomes]
rs180846	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs1974776	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1974777	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2042168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2112223	1.00[CEU][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.81[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];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2258437	0.87[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.89[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2396999	0.93[CEU][hapmap];0.90[EUR][1000 genomes]
rs2431184	0.85[ASN][1000 genomes]
rs2544859	0.93[CEU][hapmap];0.89[YRI][hapmap]
rs2544860	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2544866	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2544874	0.85[EUR][1000 genomes]
rs2544875	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2544876	0.85[EUR][1000 genomes]
rs2544880	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2544884	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2560063	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2644743	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2644744	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.88[LWK][hapmap];0.89[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.81[EUR][1000 genomes]
rs2644746	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2688186	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2688187	0.85[EUR][1000 genomes]
rs2688188	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2688189	0.85[EUR][1000 genomes]
rs2688190	0.85[EUR][1000 genomes]
rs2688191	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2688193	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2688198	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.85[EUR][1000 genomes]
rs2688199	0.82[EUR][1000 genomes]
rs2688200	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2688201	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2688206	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2688208	1.00[CEU][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs32427	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs348739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs348748	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs348749	0.86[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs348750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs348751	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs348752	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs348754	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3776984	1.00[TSI][hapmap]
rs39614	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]
rs4354100	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs454161	0.85[ASN][1000 genomes]
rs4958771	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55770418	0.80[EUR][1000 genomes]
rs56374414	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58415346	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59525998	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59749917	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6865950	1.00[TSI][hapmap]
rs6873483	0.84[ASN][1000 genomes]
rs6879277	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6884416	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6895741	1.00[TSI][hapmap]
rs702742	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73276742	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73280705	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7716019	1.00[TSI][hapmap]
rs7723269	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7728194	0.91[EUR][1000 genomes]
rs816717	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs816718	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs816720	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs816722	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs816734	0.81[ASN][1000 genomes]
rs816743	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs816747	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs960499	0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9942412	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[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
rs17116421	EBF1	cis	parietal	SCAN
rs17116421	CCDC69	cis	parietal	SCAN
rs17116421	ANXA6	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154138200-154156000	Enhancers	Primary T cells fromperipheralblood	blood
2	chr5:154144600-154157200	Enhancers	Primary T killer memory cells from peripheral blood	blood
3	chr5:154147400-154161800	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr5:154148200-154155800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr5:154148400-154154200	Enhancers	Adipose Nuclei	Adipose
6	chr5:154148400-154155400	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr5:154148400-154156000	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr5:154150200-154159400	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr5:154151200-154156000	Weak transcription	Fetal Intestine Large	intestine
10	chr5:154151200-154156800	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr5:154151200-154162200	Weak transcription	Primary hematopoietic stem cells	blood
12	chr5:154151200-154162800	Weak transcription	Primary B cells from cord blood	blood
13	chr5:154151400-154156000	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr5:154151400-154157800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:154151400-154158000	Weak transcription	HMEC	breast
16	chr5:154151400-154159400	Weak transcription	Fetal Muscle Trunk	muscle
17	chr5:154151400-154159600	Weak transcription	Thymus	Thymus
18	chr5:154151400-154161600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr5:154151600-154155600	Weak transcription	HSMM	muscle
20	chr5:154151600-154156200	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr5:154151600-154158000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr5:154151600-154158200	Weak transcription	HUVEC	blood vessel
23	chr5:154151600-154161400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr5:154151600-154161800	Weak transcription	Fetal Lung	lung
25	chr5:154151600-154162200	Weak transcription	Fetal Brain Female	brain
26	chr5:154151600-154163000	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr5:154151600-154163400	Enhancers	Primary T helper cells PMA-I stimulated	--
28	chr5:154151600-154171200	Weak transcription	Fetal Brain Male	brain
29	chr5:154151800-154158000	Weak transcription	NHLF	lung
30	chr5:154151800-154158000	Weak transcription	Osteobl	bone
31	chr5:154151800-154161800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr5:154152000-154155000	Weak transcription	Colon Smooth Muscle	Colon
33	chr5:154152200-154155800	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr5:154152200-154155800	Weak transcription	NHDF-Ad	bronchial
35	chr5:154152400-154156800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr5:154152400-154156800	Genic enhancers	K562	blood
37	chr5:154152600-154154400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
38	chr5:154152600-154154600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr5:154152600-154154800	Enhancers	Brain Hippocampus Middle	brain
40	chr5:154152600-154155000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr5:154152600-154155600	Enhancers	Primary B cells from peripheral blood	blood
42	chr5:154152600-154155800	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr5:154152600-154156000	Enhancers	H9 Cell Line	embryonic stem cell
44	chr5:154152600-154156000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr5:154152600-154156000	Enhancers	Brain Anterior Caudate	brain
46	chr5:154152600-154156400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr5:154152600-154156400	Enhancers	Ovary	ovary
48	chr5:154152600-154156600	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr5:154152600-154156800	Enhancers	Fetal Heart	heart
50	chr5:154152600-154156800	Enhancers	Skeletal Muscle Female	skeletal muscle

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