Variant report

Variant	rs2274399
Chromosome Location	chr14:39760393-39760394
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:39735564..39737850-chr14:39759651..39761816,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000150527	Chromatin interaction
ENSG00000258940	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10130008	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10131617	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs10133417	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10134365	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs10137052	0.87[ASN][1000 genomes]
rs10137352	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10137905	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.85[ASN][1000 genomes]
rs10138024	0.86[ASN][1000 genomes]
rs10138869	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs10148574	0.83[ASN][1000 genomes]
rs10148740	0.85[ASN][1000 genomes]
rs10149352	0.85[ASN][1000 genomes]
rs10151659	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10162550	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1040810	0.86[ASN][1000 genomes]
rs10872920	0.90[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs11157053	0.95[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs11157054	0.88[ASN][1000 genomes]
rs11157057	0.81[ASN][1000 genomes]
rs11157058	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11620695	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11621264	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11621330	0.91[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap]
rs11624144	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11624839	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11626679	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11627580	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12432397	0.87[ASN][1000 genomes]
rs12434140	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs12587713	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12588386	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12588728	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12880609	0.86[ASN][1000 genomes]
rs12883781	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12887525	0.85[ASN][1000 genomes]
rs12892482	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12894855	0.90[CEU][hapmap];0.86[JPT][hapmap]
rs12896838	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1570132	0.88[ASN][1000 genomes]
rs1594842	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17109021	0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap]
rs17109028	0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap]
rs17109073	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17109100	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1897792	0.86[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.82[TSI][hapmap]
rs1950952	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs1998194	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs2082635	0.91[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs2274395	0.81[JPT][hapmap]
rs2274396	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.84[ASN][1000 genomes]
rs28626340	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35065854	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35184650	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35201135	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs36057593	0.85[ASN][1000 genomes]
rs3814860	0.81[JPT][hapmap]
rs4902528	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs4902569	0.90[CEU][hapmap];0.86[JPT][hapmap];0.94[TSI][hapmap]
rs4902570	0.90[CEU][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.94[TSI][hapmap]
rs4902622	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs4902648	0.87[CHB][hapmap];0.84[CHD][hapmap];0.80[JPT][hapmap]
rs57781286	0.82[ASN][1000 genomes]
rs6571919	0.95[CHB][hapmap];0.91[JPT][hapmap]
rs7140164	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs7143646	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs7144848	0.83[ASN][1000 genomes]
rs7148150	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7150735	0.82[EUR][1000 genomes]
rs7151835	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7152341	0.81[JPT][hapmap]
rs7153482	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs719455	0.87[CHB][hapmap]
rs8004348	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8004716	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8006321	0.81[JPT][hapmap]
rs8007252	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8009651	0.81[ASN][1000 genomes]
rs8014123	0.84[ASN][1000 genomes]
rs8018717	0.95[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs910370	0.87[CHB][hapmap]
rs956108	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs956109	0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs9671943	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9671953	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][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	nsv1053133	chr14:39657535-39770729	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	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
3	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
rs2274399	PPP2R3C	cis	parietal	SCAN
rs2274399	LRFN5	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39737800-39763800	Weak transcription	Gastric	stomach
2	chr14:39738000-39763800	Weak transcription	HSMM	muscle
3	chr14:39738200-39763800	Weak transcription	Brain Angular Gyrus	brain
4	chr14:39738200-39763800	Weak transcription	HSMMtube	muscle
5	chr14:39738200-39766200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr14:39738200-39813800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr14:39738600-39763800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr14:39738800-39764800	Weak transcription	NHDF-Ad	bronchial
9	chr14:39739200-39764000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr14:39739800-39763400	Weak transcription	Lung	lung
11	chr14:39739800-39766400	Weak transcription	Aorta	Aorta
12	chr14:39741200-39764200	Weak transcription	Spleen	Spleen
13	chr14:39742000-39763400	Weak transcription	Esophagus	oesophagus
14	chr14:39744600-39769800	Weak transcription	Pancreas	Pancrea
15	chr14:39745400-39760600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr14:39745400-39764000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr14:39745600-39764000	Weak transcription	HMEC	breast
18	chr14:39746200-39776600	Weak transcription	K562	blood
19	chr14:39746400-39771200	Weak transcription	Fetal Heart	heart
20	chr14:39747200-39763800	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr14:39747800-39763600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr14:39749400-39763400	Weak transcription	Left Ventricle	heart
23	chr14:39749400-39763800	Weak transcription	Small Intestine	intestine
24	chr14:39749400-39764000	Weak transcription	Stomach Smooth Muscle	stomach
25	chr14:39749400-39764200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr14:39749400-39766400	Weak transcription	Right Ventricle	heart
27	chr14:39749400-39785400	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr14:39749600-39763400	Weak transcription	Placenta	Placenta
29	chr14:39749600-39763800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr14:39749600-39763800	Weak transcription	Brain Substantia Nigra	brain
31	chr14:39749600-39765200	Weak transcription	HUVEC	blood vessel
32	chr14:39749600-39771200	Weak transcription	Fetal Kidney	kidney
33	chr14:39750800-39762400	Weak transcription	Hela-S3	cervix
34	chr14:39752200-39763800	Weak transcription	Rectal Smooth Muscle	rectum
35	chr14:39752400-39763200	Weak transcription	Fetal Muscle Trunk	muscle
36	chr14:39752400-39763600	Weak transcription	GM12878-XiMat	blood
37	chr14:39752400-39763800	Weak transcription	Brain Anterior Caudate	brain
38	chr14:39752600-39760600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr14:39752600-39762400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr14:39752600-39763800	Weak transcription	Fetal Lung	lung
41	chr14:39752600-39764200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr14:39752600-39764200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr14:39752600-39769000	Weak transcription	Colon Smooth Muscle	Colon
44	chr14:39752600-39808200	Weak transcription	Stomach Mucosa	stomach
45	chr14:39753000-39764200	Weak transcription	A549	lung
46	chr14:39755400-39775800	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr14:39755400-39783400	Strong transcription	Liver	Liver
48	chr14:39755600-39767600	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr14:39755600-39780400	Strong transcription	HepG2	liver
50	chr14:39755600-39797200	Strong transcription	Monocytes-CD14+_RO01746	blood

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