Variant report

Variant	rs4902570
Chromosome Location	chr14:39859150-39859151
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 120 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10131617	0.86[JPT][hapmap]
rs10133417	0.90[CEU][hapmap];0.91[JPT][hapmap]
rs10134365	0.86[JPT][hapmap]
rs10137352	0.90[CEU][hapmap];0.91[JPT][hapmap]
rs10137905	0.95[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.85[JPT][hapmap];0.97[TSI][hapmap]
rs10138869	0.81[JPT][hapmap]
rs10148740	0.81[EUR][1000 genomes]
rs10149352	0.81[EUR][1000 genomes]
rs10151659	0.85[CEU][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.94[TSI][hapmap]
rs10162550	0.90[CEU][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.94[TSI][hapmap]
rs10872920	0.86[JPT][hapmap]
rs11157053	0.86[JPT][hapmap]
rs11157058	0.90[CEU][hapmap];0.90[JPT][hapmap]
rs11620695	0.90[CEU][hapmap];0.91[JPT][hapmap]
rs11621330	0.86[JPT][hapmap]
rs11626679	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs11627580	0.89[CEU][hapmap];0.90[JPT][hapmap]
rs12232110	0.87[ASN][1000 genomes]
rs12434140	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs12587625	0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12587713	0.90[CEU][hapmap];0.91[JPT][hapmap]
rs12588110	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12588175	0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12588483	0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12590172	1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12880644	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12882250	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12886769	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12887525	0.80[EUR][1000 genomes]
rs12894855	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12896502	0.82[CHB][hapmap]
rs12897960	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1594842	0.90[CEU][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.94[TSI][hapmap]
rs17109021	0.86[JPT][hapmap]
rs17109028	0.86[JPT][hapmap]
rs17109073	0.90[CEU][hapmap];0.91[JPT][hapmap];0.94[TSI][hapmap]
rs17109296	0.83[CHB][hapmap]
rs17109300	0.85[ASW][hapmap];0.82[CHB][hapmap]
rs1897792	0.86[JPT][hapmap]
rs1950336	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1950338	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1950952	0.86[JPT][hapmap]
rs1955729	0.83[CHB][hapmap]
rs1998194	0.82[JPT][hapmap]
rs2057137	0.82[CHB][hapmap]
rs2057138	0.82[CHB][hapmap]
rs2082635	0.86[JPT][hapmap]
rs2104531	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2207291	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2274395	0.85[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2274396	0.95[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs2274399	0.90[CEU][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.94[TSI][hapmap]
rs2415543	1.00[ASW][hapmap];0.80[AFR][1000 genomes]
rs2415549	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2415550	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2899889	0.85[ASN][1000 genomes]
rs34432449	0.91[AMR][1000 genomes]
rs34589600	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34649642	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs34894621	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34928332	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35115885	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35459433	0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs35553183	0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs35693868	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs35876588	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35904659	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs36010374	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs36057593	0.81[EUR][1000 genomes]
rs3814860	0.85[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4899245	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4899277	0.91[AMR][1000 genomes]
rs4899278	0.91[AMR][1000 genomes]
rs4902528	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs4902569	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4902598	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4902599	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4902622	0.85[ASW][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4902636	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4902637	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4902648	0.85[ASW][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.82[TSI][hapmap];0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4902665	0.90[ASN][1000 genomes]
rs4902676	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4902692	0.82[CHB][hapmap]
rs56046902	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs56375627	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57781286	0.81[EUR][1000 genomes]
rs6571919	0.86[JPT][hapmap]
rs6571926	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs67439322	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67963654	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7140164	0.81[JPT][hapmap]
rs71407788	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs71407789	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7140983	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7143646	0.90[JPT][hapmap]
rs7145821	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7148150	0.90[CEU][hapmap];0.91[JPT][hapmap]
rs7148377	0.95[CHB][hapmap];0.87[JPT][hapmap]
rs7152341	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7152935	0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7153413	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7153482	0.81[JPT][hapmap]
rs7161403	1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs718364	0.95[CHB][hapmap];0.82[CHD][hapmap];0.87[JPT][hapmap]
rs719455	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs72675487	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs8003397	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs8003621	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs8004716	0.90[CEU][hapmap];0.91[JPT][hapmap]
rs8006123	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs8006321	0.85[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs8007252	0.82[EUR][1000 genomes]
rs8018717	0.86[JPT][hapmap]
rs910370	0.91[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs910371	0.91[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9332387	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs956109	0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037183	chr14:39736939-39949233	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv542048	chr14:39736939-39949233	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4902570	PPP2R3C	cis	parietal	SCAN
rs4902570	CTAGE5	cis	multi-tissue	Pritchard

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39770800-39872400	Weak transcription	Colonic Mucosa	Colon
2	chr14:39818800-39867200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr14:39835400-39872400	Weak transcription	Fetal Muscle Leg	muscle
4	chr14:39836200-39872800	Weak transcription	Esophagus	oesophagus
5	chr14:39836400-39870600	Weak transcription	Gastric	stomach
6	chr14:39840000-39863200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr14:39840000-39863400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr14:39840000-39864000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr14:39840000-39867000	Weak transcription	Left Ventricle	heart
10	chr14:39840000-39867400	Weak transcription	Pancreas	Pancrea
11	chr14:39840000-39882600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr14:39840200-39867200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr14:39840600-39864400	Weak transcription	Primary B cells from peripheral blood	blood
14	chr14:39841000-39865800	Weak transcription	Primary B cells from cord blood	blood
15	chr14:39841200-39867000	Weak transcription	Duodenum Mucosa	Duodenum
16	chr14:39841400-39862800	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr14:39846200-39864800	Weak transcription	NHEK	skin
18	chr14:39846200-39878800	Weak transcription	Right Ventricle	heart
19	chr14:39846400-39862400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr14:39846400-39864600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr14:39846400-39867200	Weak transcription	Primary hematopoietic stem cells	blood
22	chr14:39846600-39862600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr14:39846600-39864600	Weak transcription	HepG2	liver
24	chr14:39846600-39864600	Weak transcription	NH-A	brain
25	chr14:39846600-39864800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr14:39846600-39866600	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr14:39846800-39862600	Weak transcription	Adipose Nuclei	Adipose
28	chr14:39846800-39872400	Weak transcription	HSMMtube	muscle
29	chr14:39848000-39862600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr14:39850400-39870800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr14:39851000-39866800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr14:39851200-39866000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr14:39851200-39868600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr14:39851400-39868600	Weak transcription	Brain Hippocampus Middle	brain
35	chr14:39851400-39868600	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr14:39851600-39862400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr14:39851800-39864600	Weak transcription	Fetal Intestine Large	intestine
38	chr14:39852800-39863400	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr14:39852800-39864600	Weak transcription	Dnd41	blood
40	chr14:39853000-39867400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr14:39853000-39867400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr14:39853200-39866200	Weak transcription	GM12878-XiMat	blood
43	chr14:39853200-39867800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr14:39853600-39862800	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr14:39853600-39866200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr14:39853600-39867200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr14:39853600-39874200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
48	chr14:39853800-39863600	Weak transcription	Primary T cells from cord blood	blood
49	chr14:39854400-39872600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr14:39855200-39863400	Weak transcription	Spleen	Spleen

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