Variant report

Variant	rs17214952
Chromosome Location	chr3:46011436-46011437
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 160 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:157)

rs_ID	r²[population]
rs13059238	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13060287	0.86[EUR][1000 genomes]
rs13063527	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13063635	0.81[AMR][1000 genomes]
rs13066062	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13066516	0.95[EUR][1000 genomes]
rs13068570	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13069079	1.00[CEU][hapmap];0.93[GIH][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13069742	0.82[EUR][1000 genomes]
rs13071283	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13072267	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13074382	1.00[CEU][hapmap];0.95[GIH][hapmap];0.86[EUR][1000 genomes]
rs13075528	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13075758	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13078739	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13079869	1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13081151	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13081213	0.90[CEU][hapmap];0.95[GIH][hapmap];0.86[EUR][1000 genomes]
rs13082697	0.86[EUR][1000 genomes]
rs13085367	0.81[AMR][1000 genomes]
rs13089554	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13089855	0.89[EUR][1000 genomes]
rs13090194	1.00[CEU][hapmap];0.95[GIH][hapmap];0.86[EUR][1000 genomes]
rs13091868	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13093179	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13095602	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13095717	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13096741	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs13097556	0.86[EUR][1000 genomes]
rs13099120	0.95[EUR][1000 genomes]
rs13433997	0.89[EUR][1000 genomes]
rs1491950	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1491951	0.82[EUR][1000 genomes]
rs17215008	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17215981	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17280623	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17330872	1.00[CEU][hapmap];0.97[GIH][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17714101	0.89[CEU][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes]
rs17714228	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs17764831	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs17764980	0.89[CEU][hapmap];0.89[EUR][1000 genomes]
rs1994491	0.89[CEU][hapmap];0.95[EUR][1000 genomes]
rs1994492	0.94[EUR][1000 genomes]
rs1994493	0.94[EUR][1000 genomes]
rs2088690	0.86[EUR][1000 genomes]
rs2088692	0.86[EUR][1000 genomes]
rs2102055	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2102056	0.82[EUR][1000 genomes]
rs2171531	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2230322	1.00[CEU][hapmap];0.95[GIH][hapmap];0.86[EUR][1000 genomes]
rs2373087	0.95[EUR][1000 genomes]
rs33910087	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34000569	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34047915	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34068335	0.94[EUR][1000 genomes]
rs34093271	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34127208	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34168660	0.86[EUR][1000 genomes]
rs34283240	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34324101	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34339943	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34340587	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34381952	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34438204	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34442130	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34452002	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34460587	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34492478	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34493660	0.89[EUR][1000 genomes]
rs34518147	0.82[EUR][1000 genomes]
rs34562820	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34584867	0.86[EUR][1000 genomes]
rs34619093	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34679077	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34718164	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34754340	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34766614	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34774687	0.86[EUR][1000 genomes]
rs34836513	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34849862	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34863575	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34901975	0.80[EUR][1000 genomes]
rs35110864	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35159820	0.86[EUR][1000 genomes]
rs35161099	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35209528	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35280891	0.84[EUR][1000 genomes]
rs35334665	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35454877	0.86[EUR][1000 genomes]
rs35464221	0.81[AMR][1000 genomes]
rs35477280	0.95[EUR][1000 genomes]
rs35501575	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35516580	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35525815	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35539222	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35581648	0.81[AMR][1000 genomes]
rs35669129	1.00[CEU][hapmap];0.95[GIH][hapmap];0.86[EUR][1000 genomes]
rs35751180	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35772789	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35814488	0.86[EUR][1000 genomes]
rs35827997	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35831747	0.95[EUR][1000 genomes]
rs35855315	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35883205	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35921206	0.86[EUR][1000 genomes]
rs35930050	0.86[EUR][1000 genomes]
rs36023124	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs36039366	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs36040135	0.86[EUR][1000 genomes]
rs36057789	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs36122610	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3851346	1.00[CEU][hapmap];0.95[GIH][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs41289616	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs41289622	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4362758	0.86[EUR][1000 genomes]
rs4373103	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4388012	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs55875328	0.89[EUR][1000 genomes]
rs55920693	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs56332428	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs60019065	0.86[EUR][1000 genomes]
rs61556067	0.89[EUR][1000 genomes]
rs61650989	0.89[EUR][1000 genomes]
rs67200151	0.89[EUR][1000 genomes]
rs6780028	0.86[EUR][1000 genomes]
rs6785091	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs6790866	0.86[EUR][1000 genomes]
rs6791016	0.86[EUR][1000 genomes]
rs67937868	0.89[EUR][1000 genomes]
rs68087193	0.84[EUR][1000 genomes]
rs71325091	0.85[EUR][1000 genomes]
rs71325092	0.89[EUR][1000 genomes]
rs71325095	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs71325096	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71325098	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs71325100	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs71325101	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71325102	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71327003	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs71327006	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71327007	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71327009	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71327010	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71327014	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs71327015	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs71327017	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs71327021	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs71327023	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs71327024	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs71327025	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs71327027	0.81[AMR][1000 genomes]
rs71615438	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs876668	0.86[EUR][1000 genomes]
rs9824651	0.82[EUR][1000 genomes]
rs9825081	0.82[EUR][1000 genomes]
rs9845382	0.82[EUR][1000 genomes]
rs9877748	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv876736	chr3:45900621-46027410	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17214952	CDC25A	cis	cerebellum	SCAN
rs17214952	PTPN23	cis	parietal	SCAN
rs17214952	LIMD1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:45980800-46013400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
2	chr3:45981600-46025000	Strong transcription	Fetal Intestine Large	intestine
3	chr3:45983200-46012400	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr3:45986400-46012200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr3:45986400-46026600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr3:45986600-46012000	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr3:45986600-46026800	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr3:45986800-46012200	Strong transcription	Primary B cells from peripheral blood	blood
9	chr3:45987200-46013600	Strong transcription	Primary hematopoietic stem cells	blood
10	chr3:45987200-46027200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:45987400-46026600	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr3:45987800-46012200	Strong transcription	HepG2	liver
13	chr3:45987800-46026400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr3:45987800-46026800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:45987800-46027200	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr3:45988000-46012000	Strong transcription	H1 Cell Line	embryonic stem cell
17	chr3:45988000-46026600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr3:45988200-46012000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:45988800-46011800	Strong transcription	Lung	lung
20	chr3:45989400-46013800	Strong transcription	Dnd41	blood
21	chr3:45990600-46017200	Strong transcription	Rectal Mucosa Donor 29	rectum
22	chr3:45991200-46012000	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr3:45991200-46017400	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr3:45992600-46013200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr3:45992600-46013600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr3:45993000-46013600	Strong transcription	Thymus	Thymus
27	chr3:45996200-46025400	Strong transcription	Liver	Liver
28	chr3:45999200-46011600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr3:45999200-46011800	Strong transcription	H9 Cell Line	embryonic stem cell
30	chr3:45999200-46011800	Strong transcription	Pancreas	Pancrea
31	chr3:45999200-46012200	Genic enhancers	Primary T cells fromperipheralblood	blood
32	chr3:45999400-46012000	Strong transcription	Ovary	ovary
33	chr3:45999400-46018200	Strong transcription	Fetal Lung	lung
34	chr3:46000000-46029600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
35	chr3:46001000-46012200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr3:46002000-46014200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr3:46002200-46011800	Strong transcription	Spleen	Spleen
38	chr3:46002200-46018600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:46002400-46012800	Strong transcription	Cortex derived primary cultured neurospheres	brain
40	chr3:46002600-46025000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr3:46002600-46027200	Weak transcription	A549	lung
42	chr3:46003200-46012200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr3:46003600-46014800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr3:46007400-46014000	Weak transcription	HUVEC	blood vessel
45	chr3:46007600-46011800	Strong transcription	Fetal Intestine Small	intestine
46	chr3:46007800-46012200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr3:46007800-46024200	Weak transcription	Fetal Kidney	kidney
48	chr3:46008000-46011600	Strong transcription	Duodenum Mucosa	Duodenum
49	chr3:46008000-46012000	Strong transcription	Primary T cells from cord blood	blood
50	chr3:46008000-46013000	Strong transcription	GM12878-XiMat	blood

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