Variant report

Variant	rs17116411
Chromosome Location	chr5:154142057-154142058
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:154138655..154140454-chr5:154140669..154142332,2	MCF-7	breast:
2	chr5:154034090..154035820-chr5:154141862..154143840,2	K562	blood:
3	chr5:154141399..154144040-chr5:154148555..154150698,2	MCF-7	breast:
4	chr5:154032703..154035820-chr5:154141862..154144774,3	K562	blood:

Extended variants
information (count: 88 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1035368	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][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];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12300	0.87[CEU][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.90[TSI][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]
rs17116414	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17116417	1.00[TSI][hapmap]
rs17116421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17116433	1.00[CHB][hapmap]
rs17116442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17116534	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs180846	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.80[EUR][1000 genomes]
rs1974776	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]
rs1974777	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]
rs2042168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2112223	1.00[CEU][hapmap];0.86[JPT][hapmap];0.81[EUR][1000 genomes]
rs2161128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2258437	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2396999	0.93[CEU][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2431184	0.85[ASN][1000 genomes]
rs2544860	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs2544866	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2544874	0.85[EUR][1000 genomes]
rs2544875	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2544876	0.85[EUR][1000 genomes]
rs2544880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[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];0.83[YRI][hapmap];0.80[EUR][1000 genomes]
rs2560063	0.84[EUR][1000 genomes]
rs2644743	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2644744	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes]
rs2644746	0.80[EUR][1000 genomes]
rs2688186	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2688187	0.85[EUR][1000 genomes]
rs2688188	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	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs2688199	0.82[EUR][1000 genomes]
rs2688200	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2688201	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2688206	0.85[EUR][1000 genomes]
rs2688208	1.00[CEU][hapmap];0.86[JPT][hapmap];0.84[EUR][1000 genomes]
rs32427	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs348739	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs348748	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs348749	0.86[CEU][hapmap];1.00[CHB][hapmap];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];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs348751	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs348752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs348754	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3776984	1.00[TSI][hapmap]
rs39614	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];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4354100	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	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58415346	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59525998	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59749917	0.92[AFR][1000 genomes];1.00[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	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6884416	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6895741	1.00[TSI][hapmap]
rs702742	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73276742	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73280705	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7716019	1.00[TSI][hapmap]
rs7723269	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7728194	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs816717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs816718	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs816720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs816722	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs816734	0.81[ASN][1000 genomes]
rs816743	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	0.88[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	nsv1021153	chr5:154099869-154147970	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17116411	CCDC69	cis	parietal	SCAN
rs17116411	POMZP3	trans	lymphoblastoid	seeQTL
rs17116411	ANXA6	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154137200-154142400	Enhancers	Primary B cells from peripheral blood	blood
2	chr5:154137800-154144000	Enhancers	Sigmoid Colon	Sigmoid Colon
3	chr5:154138000-154142200	Enhancers	Liver	Liver
4	chr5:154138000-154142400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr5:154138000-154142400	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr5:154138000-154142600	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr5:154138200-154142200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr5:154138200-154142400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr5:154138200-154142400	Enhancers	Brain Hippocampus Middle	brain
10	chr5:154138200-154146000	Weak transcription	Placenta	Placenta
11	chr5:154138200-154151400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr5:154138200-154156000	Enhancers	Primary T cells fromperipheralblood	blood
13	chr5:154138400-154142200	Enhancers	Rectal Smooth Muscle	rectum
14	chr5:154138400-154142400	Enhancers	Colon Smooth Muscle	Colon
15	chr5:154138400-154142400	Enhancers	Psoas Muscle	Psoas
16	chr5:154138400-154142600	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr5:154138400-154142600	Enhancers	Fetal Heart	heart
18	chr5:154138400-154147800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr5:154138800-154142400	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr5:154138800-154142600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr5:154138800-154142600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr5:154138800-154150000	Weak transcription	HSMM	muscle
23	chr5:154139000-154142400	Enhancers	HepG2	liver
24	chr5:154139000-154142800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr5:154139000-154147200	Weak transcription	NH-A	brain
26	chr5:154139000-154149800	Weak transcription	NHLF	lung
27	chr5:154139200-154145600	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr5:154139400-154142200	Enhancers	H1 Cell Line	embryonic stem cell
29	chr5:154139400-154145400	Weak transcription	Fetal Kidney	kidney
30	chr5:154139600-154142200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
31	chr5:154139600-154142200	Enhancers	Left Ventricle	heart
32	chr5:154139600-154143200	Enhancers	Right Atrium	heart
33	chr5:154139600-154148600	Weak transcription	Fetal Intestine Large	intestine
34	chr5:154139800-154142200	Enhancers	Stomach Mucosa	stomach
35	chr5:154139800-154148800	Weak transcription	Fetal Brain Male	brain
36	chr5:154140000-154142400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr5:154140000-154145800	Weak transcription	Fetal Stomach	stomach
38	chr5:154140200-154142200	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr5:154140200-154142200	Enhancers	Brain Angular Gyrus	brain
40	chr5:154140200-154142200	Enhancers	Pancreas	Pancrea
41	chr5:154140200-154142400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr5:154140200-154149200	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr5:154140400-154142200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr5:154140400-154142200	Enhancers	Right Ventricle	heart
45	chr5:154140400-154142400	Enhancers	Brain Germinal Matrix	brain
46	chr5:154140400-154142600	Enhancers	Brain Substantia Nigra	brain
47	chr5:154140600-154142200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
48	chr5:154140600-154142400	Genic enhancers	K562	blood
49	chr5:154140800-154142200	Enhancers	Aorta	Aorta
50	chr5:154140800-154142400	Enhancers	Stomach Smooth Muscle	stomach

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