Variant report

Variant	rs2290697
Chromosome Location	chr5:52978722-52978723
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10940327	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.98[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];0.99[ASN][1000 genomes]
rs11749138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11949787	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11956779	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12514303	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12517465	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12518490	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12522861	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2087618	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2124948	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2168662	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs269414	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28507151	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35879821	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4147736	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4362905	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55689727	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55791118	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56185221	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56402244	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs567	1.00[ASW][hapmap];1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60308929	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6450150	0.89[CHB][hapmap]
rs6450151	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6860913	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6897299	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72751836	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72753643	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72757399	0.82[ASN][1000 genomes]
rs7712013	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7723495	0.83[CHB][hapmap]
rs7737530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752745	chr5:52422063-53343529	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1032632	chr5:52667145-53655624	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv880868	chr5:52799618-53002783	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv880689	chr5:52847995-53002783	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv881604	chr5:52885100-53035301	Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1032504	chr5:52908394-53398435	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv537763	chr5:52908394-53398435	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv880673	chr5:52965574-53002783	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv881152	chr5:52965574-53028303	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv881028	chr5:52965574-53035301	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv880806	chr5:52967967-53002783	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv880377	chr5:52967967-53028303	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv881185	chr5:52967967-53060893	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv830298	chr5:52973912-53193398	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2290697	NDUFS4	cis	parietal	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52920800-52978800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr5:52929000-52981800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr5:52940000-52982000	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr5:52941400-52980200	Weak transcription	HepG2	liver
5	chr5:52941400-52985200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr5:52945400-52979000	Weak transcription	HMEC	breast
7	chr5:52945400-52980200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr5:52945400-52980800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr5:52945400-52981000	Weak transcription	Psoas Muscle	Psoas
10	chr5:52945400-52985000	Weak transcription	Brain Hippocampus Middle	brain
11	chr5:52945600-52980800	Weak transcription	GM12878-XiMat	blood
12	chr5:52945600-52981600	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr5:52945600-52983000	Weak transcription	Fetal Muscle Trunk	muscle
14	chr5:52945600-52983600	Weak transcription	Fetal Thymus	thymus
15	chr5:52946800-52981400	Weak transcription	NHEK	skin
16	chr5:52955800-52982200	Weak transcription	Dnd41	blood
17	chr5:52956000-52982600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr5:52961600-52978800	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr5:52961600-52984200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr5:52961800-52978800	Weak transcription	Stomach Smooth Muscle	stomach
21	chr5:52961800-52979800	Weak transcription	Aorta	Aorta
22	chr5:52961800-52979800	Weak transcription	Fetal Muscle Leg	muscle
23	chr5:52961800-52989200	Weak transcription	Ovary	ovary
24	chr5:52962400-52979000	Weak transcription	NHDF-Ad	bronchial
25	chr5:52962400-52979800	Weak transcription	Pancreas	Pancrea
26	chr5:52962600-52980600	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr5:52963600-52984400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr5:52963800-52979800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr5:52965400-52980600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr5:52967600-52979400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr5:52968000-52980600	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr5:52968000-52983400	Weak transcription	Duodenum Mucosa	Duodenum
33	chr5:52968600-52980800	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr5:52968800-52980200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr5:52970200-52984800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr5:52971400-52980600	Weak transcription	Fetal Intestine Large	intestine
37	chr5:52972600-52978800	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr5:52972600-52980800	Weak transcription	Colon Smooth Muscle	Colon
39	chr5:52973000-52983600	Weak transcription	Brain Anterior Caudate	brain
40	chr5:52974400-52983200	Weak transcription	Spleen	Spleen
41	chr5:52974600-52978800	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr5:52974800-52980200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr5:52975200-52979000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr5:52975400-52981000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr5:52975600-52979200	Weak transcription	Primary T cells from cord blood	blood
46	chr5:52975600-52982400	Weak transcription	Osteobl	bone
47	chr5:52975800-52979600	Weak transcription	HSMMtube	muscle
48	chr5:52975800-52980200	Weak transcription	HSMM	muscle
49	chr5:52976000-52980200	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr5:52976000-52982400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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