Variant report

Variant	rs2274395
Chromosome Location	chr14:39865764-39865765
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:39863679..39866001-chr14:39899899..39901837,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000165355	Chromatin interaction

Extended variants
information (count: 126 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs10131617	0.81[JPT][hapmap]
rs10133417	0.86[JPT][hapmap]
rs10134365	0.81[JPT][hapmap]
rs10137352	0.86[JPT][hapmap]
rs10137905	0.82[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.80[TSI][hapmap]
rs10151659	0.82[JPT][hapmap]
rs10162550	0.86[JPT][hapmap]
rs10872920	0.81[JPT][hapmap]
rs11157053	0.81[JPT][hapmap]
rs11157058	0.86[JPT][hapmap]
rs11157067	0.86[AFR][1000 genomes]
rs11620695	0.86[JPT][hapmap]
rs11621330	0.81[JPT][hapmap]
rs11626679	0.82[JPT][hapmap]
rs11627580	0.85[JPT][hapmap]
rs11847057	0.93[AFR][1000 genomes]
rs12232110	0.95[ASN][1000 genomes]
rs12434140	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs12587625	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12587713	0.86[JPT][hapmap]
rs12588110	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12588175	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12588483	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12589427	0.95[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs12590172	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12880644	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12882250	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12883652	0.85[ASN][1000 genomes]
rs12884747	0.95[AFR][1000 genomes]
rs12886769	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12894855	1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12896502	0.82[CHB][hapmap]
rs12897960	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1594842	0.86[JPT][hapmap]
rs17109021	0.81[JPT][hapmap]
rs17109028	0.81[JPT][hapmap]
rs17109073	0.86[JPT][hapmap]
rs17109296	0.83[CHB][hapmap]
rs17109300	1.00[ASW][hapmap];0.82[CHB][hapmap];0.81[GIH][hapmap];0.97[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs17109328	0.94[AFR][1000 genomes]
rs1897792	0.81[JPT][hapmap]
rs1950329	0.95[AFR][1000 genomes]
rs1950334	0.93[AFR][1000 genomes]
rs1950336	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1950338	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1950952	0.81[JPT][hapmap]
rs1955718	0.95[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1955729	0.83[CHB][hapmap]
rs2038278	0.85[ASN][1000 genomes]
rs2057137	0.82[CHB][hapmap];0.81[GIH][hapmap];0.87[LWK][hapmap];0.83[MKK][hapmap]
rs2057138	0.82[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs2082635	0.81[JPT][hapmap]
rs2104531	0.81[ASN][1000 genomes]
rs2207291	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2274396	0.82[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap]
rs2274399	0.81[JPT][hapmap]
rs2415543	0.85[ASW][hapmap];0.85[MEX][hapmap]
rs2415549	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2415550	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2899888	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2899889	0.92[ASN][1000 genomes]
rs34432449	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34589600	0.80[ASN][1000 genomes]
rs34649642	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34687394	0.95[AFR][1000 genomes]
rs34894621	0.80[ASN][1000 genomes]
rs34928332	0.82[ASN][1000 genomes]
rs35115885	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs35459433	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35553183	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35643160	0.95[AFR][1000 genomes]
rs35693868	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35876588	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs35923045	0.94[AFR][1000 genomes]
rs36010374	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3814860	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][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];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4899245	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4899277	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4899278	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4899291	0.94[AFR][1000 genomes]
rs4902528	0.87[CHB][hapmap]
rs4902569	0.85[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4902570	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]
rs4902598	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4902599	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4902622	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4902636	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4902637	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4902648	1.00[ASW][hapmap];0.95[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4902665	0.96[AFR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4902676	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4902692	0.82[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs56046902	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56375627	0.80[ASN][1000 genomes]
rs6571919	0.81[JPT][hapmap]
rs67439322	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs67963654	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs71407788	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs71407789	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7140983	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7143646	0.85[JPT][hapmap]
rs7145821	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7148150	0.86[JPT][hapmap]
rs7148377	0.95[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs7152341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7152935	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7153413	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7158709	0.95[AFR][1000 genomes]
rs7161403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs718364	0.95[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs719455	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap]
rs72675487	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8003397	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8003621	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8004716	0.86[JPT][hapmap]
rs8006123	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8006321	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8012768	0.86[MEX][hapmap]
rs8018717	0.81[JPT][hapmap]
rs8020250	0.94[AFR][1000 genomes]
rs910370	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs910371	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9332387	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs956109	0.81[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
rs2274395	LRFN5	cis	cerebellum	SCAN
rs2274395	PPP2R3C	cis	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

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	chr14:39840000-39867000	Weak transcription	Left Ventricle	heart
7	chr14:39840000-39867400	Weak transcription	Pancreas	Pancrea
8	chr14:39840000-39882600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr14:39840200-39867200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr14:39841000-39865800	Weak transcription	Primary B cells from cord blood	blood
11	chr14:39841200-39867000	Weak transcription	Duodenum Mucosa	Duodenum
12	chr14:39846200-39878800	Weak transcription	Right Ventricle	heart
13	chr14:39846400-39867200	Weak transcription	Primary hematopoietic stem cells	blood
14	chr14:39846600-39866600	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr14:39846800-39872400	Weak transcription	HSMMtube	muscle
16	chr14:39850400-39870800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr14:39851000-39866800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr14:39851200-39866000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr14:39851200-39868600	Weak transcription	Brain Cingulate Gyrus	brain
20	chr14:39851400-39868600	Weak transcription	Brain Hippocampus Middle	brain
21	chr14:39851400-39868600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr14:39853000-39867400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr14:39853000-39867400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr14:39853200-39866200	Weak transcription	GM12878-XiMat	blood
25	chr14:39853200-39867800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr14:39853600-39866200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr14:39853600-39867200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr14:39853600-39874200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr14:39854400-39872600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr14:39855400-39868800	Weak transcription	Aorta	Aorta
31	chr14:39856200-39867200	Weak transcription	Thymus	Thymus
32	chr14:39857000-39870400	Weak transcription	Brain Germinal Matrix	brain
33	chr14:39858600-39866200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr14:39860000-39867000	Weak transcription	Ovary	ovary
35	chr14:39860200-39882200	Weak transcription	Fetal Heart	heart
36	chr14:39860400-39868600	Weak transcription	A549	lung
37	chr14:39860600-39866000	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr14:39860600-39867200	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr14:39860800-39868400	Weak transcription	Stomach Smooth Muscle	stomach
40	chr14:39861000-39867200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr14:39861000-39868400	Weak transcription	Hela-S3	cervix
42	chr14:39861200-39871800	Weak transcription	Fetal Brain Male	brain
43	chr14:39861200-39872200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr14:39861400-39866200	Weak transcription	Placenta	Placenta
45	chr14:39861400-39868000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr14:39861400-39874000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr14:39861600-39866000	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr14:39861600-39867000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr14:39861800-39872000	Weak transcription	K562	blood
50	chr14:39862000-39867200	Weak transcription	HUES6 Cell Line	embryonic stem cell

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