Variant report

Variant	rs2274396
Chromosome Location	chr14:39815491-39815492
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10130008	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10131617	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs10133417	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10134365	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs10137052	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10137352	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10137905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10138869	0.91[JPT][hapmap]
rs10148574	0.94[ASN][1000 genomes]
rs10148740	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10149352	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10151659	0.90[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap]
rs10162550	0.95[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap]
rs10872920	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs11157053	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs11157058	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11157061	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11620695	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11621330	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs11624144	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11624839	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11626679	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11627580	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12434140	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs12587713	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs12588386	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12590172	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs12880609	0.90[ASN][1000 genomes]
rs12883781	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12887525	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12894855	0.95[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes]
rs12896502	0.82[CHB][hapmap]
rs12896838	0.84[ASN][1000 genomes]
rs1594842	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap];0.97[TSI][hapmap]
rs17109021	0.91[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap]
rs17109028	0.91[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap]
rs17109073	0.95[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap]
rs17109100	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17109300	0.82[CHB][hapmap];0.80[CHD][hapmap]
rs1897792	0.82[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap]
rs1950952	0.95[JPT][hapmap]
rs1998194	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs2057137	0.82[CHB][hapmap];0.80[CHD][hapmap]
rs2057138	0.82[CHB][hapmap]
rs2082635	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs2104531	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2274395	0.82[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap]
rs2274399	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]
rs34589600	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34894621	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34928332	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35115885	0.83[EUR][1000 genomes]
rs35876588	0.83[EUR][1000 genomes]
rs35904659	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36057593	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3814860	0.82[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap]
rs4899227	0.80[ASN][1000 genomes]
rs4902528	0.87[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs4902569	0.95[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs4902570	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]
rs4902622	0.91[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap]
rs4902648	0.87[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap]
rs4902692	0.82[CHB][hapmap]
rs56375627	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57781286	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6571919	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs6571926	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67439322	0.83[EUR][1000 genomes]
rs67963654	0.83[EUR][1000 genomes]
rs7140164	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs7143646	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs7144848	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7145821	0.83[EUR][1000 genomes]
rs7148150	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7151835	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7152341	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs7153482	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs7161403	0.82[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap];0.81[TSI][hapmap]
rs719455	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs8004716	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8006321	0.82[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap]
rs8007252	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8014123	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8018717	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs910370	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs956108	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs956109	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs9671943	0.81[ASN][1000 genomes]
rs9671953	0.82[ASN][1000 genomes]

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
rs2274396	LRFN5	cis	cerebellum	SCAN
rs2274396	CTAGE5	cis	multi-tissue	Pritchard

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:39756200-39828400	Weak transcription	Brain Germinal Matrix	brain
2	chr14:39756600-39819600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr14:39757400-39843800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr14:39764600-39818400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr14:39767200-39833800	Weak transcription	Small Intestine	intestine
6	chr14:39770000-39816400	Weak transcription	Colon Smooth Muscle	Colon
7	chr14:39770600-39819800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr14:39770800-39872400	Weak transcription	Colonic Mucosa	Colon
9	chr14:39786600-39828600	Weak transcription	Spleen	Spleen
10	chr14:39786800-39823000	Strong transcription	Liver	Liver
11	chr14:39792800-39841600	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr14:39793000-39822200	Weak transcription	Fetal Lung	lung
13	chr14:39794400-39843200	Weak transcription	HUVEC	blood vessel
14	chr14:39796400-39817800	Weak transcription	HSMMtube	muscle
15	chr14:39796400-39828400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr14:39797000-39837400	Weak transcription	Brain Substantia Nigra	brain
17	chr14:39797600-39816000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr14:39802000-39835600	Weak transcription	Esophagus	oesophagus
19	chr14:39802000-39841200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr14:39802600-39817000	Weak transcription	NHLF	lung
21	chr14:39802600-39835400	Weak transcription	Psoas Muscle	Psoas
22	chr14:39802800-39822000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr14:39802800-39828400	Weak transcription	Ovary	ovary
24	chr14:39802800-39828400	Weak transcription	Pancreas	Pancrea
25	chr14:39802800-39828600	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr14:39802800-39835400	Weak transcription	Gastric	stomach
27	chr14:39802800-39839400	Weak transcription	Aorta	Aorta
28	chr14:39803000-39816000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr14:39803000-39835400	Weak transcription	Right Ventricle	heart
30	chr14:39803000-39845800	Weak transcription	NHEK	skin
31	chr14:39803200-39816000	Weak transcription	Primary hematopoietic stem cells	blood
32	chr14:39803200-39816200	Weak transcription	Fetal Muscle Leg	muscle
33	chr14:39803200-39818000	Weak transcription	Brain Angular Gyrus	brain
34	chr14:39803200-39824600	Weak transcription	Brain Hippocampus Middle	brain
35	chr14:39803200-39833000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr14:39803200-39838400	Weak transcription	Thymus	Thymus
37	chr14:39803200-39843400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr14:39803200-39845800	Weak transcription	Brain Cingulate Gyrus	brain
39	chr14:39803400-39815600	Weak transcription	Fetal Kidney	kidney
40	chr14:39803400-39815800	Weak transcription	Stomach Smooth Muscle	stomach
41	chr14:39803400-39816000	Weak transcription	Fetal Thymus	thymus
42	chr14:39803400-39843800	Weak transcription	HMEC	breast
43	chr14:39803600-39816000	Weak transcription	Fetal Muscle Trunk	muscle
44	chr14:39804000-39816000	Weak transcription	Lung	lung
45	chr14:39806800-39816000	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr14:39807000-39815600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr14:39807000-39816200	Weak transcription	Osteobl	bone
48	chr14:39807000-39824400	Weak transcription	NH-A	brain
49	chr14:39807400-39836000	Weak transcription	Brain Anterior Caudate	brain
50	chr14:39808400-39819000	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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