Variant report

Variant	rs6874840
Chromosome Location	chr5:99897866-99897867
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10043796	1.00[ASN][1000 genomes]
rs10044020	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10053309	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10054480	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10054650	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10491366	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13179756	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17447382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17774525	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1993517	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2036562	1.00[ASN][1000 genomes]
rs34462099	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34550123	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35068466	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3911547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55825520	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55895019	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68104976	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6869843	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6871027	0.87[ASN][1000 genomes]
rs6872159	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6879886	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6890035	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6892505	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6898051	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72774688	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7714303	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9327206	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599165	chr5:99469004-100063039	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv948969	chr5:99534096-100133827	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1021183	chr5:99625857-100221426	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
4	nsv882461	chr5:99745767-99927338	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv882462	chr5:99745767-100060150	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv1025890	chr5:99745775-99936186	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv1017420	chr5:99745775-100133140	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	nsv537825	chr5:99745775-100133140	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv882463	chr5:99784116-99898851	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv882464	chr5:99784116-99905367	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv882465	chr5:99784116-99927338	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
12	nsv1018395	chr5:99827242-100003207	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	esv2763473	chr5:99883352-99907664	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6874840	KATNAL2	trans	parietal	SCAN
rs6874840	UNQ1912	cis	multi-tissue	Pritchard

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:99872400-99931400	Weak transcription	Aorta	Aorta
2	chr5:99872600-99922800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr5:99872800-99902000	Weak transcription	HSMM	muscle
4	chr5:99872800-99916200	Weak transcription	Ovary	ovary
5	chr5:99873400-99916200	Weak transcription	Fetal Stomach	stomach
6	chr5:99873400-99930600	Weak transcription	NH-A	brain
7	chr5:99878400-99930600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr5:99882200-99899200	Weak transcription	Left Ventricle	heart
9	chr5:99884000-99910400	Weak transcription	HUVEC	blood vessel
10	chr5:99886800-99899400	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr5:99886800-99930200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr5:99887200-99912000	Weak transcription	Psoas Muscle	Psoas
13	chr5:99887200-99916200	Weak transcription	Lung	lung
14	chr5:99887200-99924600	Weak transcription	Fetal Thymus	thymus
15	chr5:99887600-99899600	Weak transcription	Fetal Muscle Leg	muscle
16	chr5:99887600-99907200	Weak transcription	Pancreas	Pancrea
17	chr5:99887800-99898200	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr5:99889600-99898800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr5:99889800-99898200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr5:99889800-99898600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr5:99893800-99910400	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr5:99894400-99907400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr5:99894800-99899400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr5:99895000-99899000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr5:99895400-99898400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr5:99895400-99902000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr5:99895400-99919800	Weak transcription	HSMMtube	muscle
28	chr5:99895600-99903000	Weak transcription	Placenta	Placenta
29	chr5:99895800-99911600	Weak transcription	NHDF-Ad	bronchial
30	chr5:99895800-99921000	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr5:99895800-99931000	Weak transcription	Fetal Intestine Large	intestine
32	chr5:99896200-99898000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr5:99896200-99898600	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr5:99896200-99916200	Weak transcription	Fetal Muscle Trunk	muscle
35	chr5:99896200-99927600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr5:99896400-99899000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr5:99896400-99899000	Weak transcription	Liver	Liver
38	chr5:99896400-99903600	Weak transcription	Fetal Kidney	kidney
39	chr5:99896600-99933800	Weak transcription	Primary hematopoietic stem cells	blood
40	chr5:99896800-99898400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr5:99896800-99898400	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr5:99896800-99902400	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr5:99896800-99903000	Weak transcription	Osteobl	bone
44	chr5:99896800-99931000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr5:99897000-99898200	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr5:99897000-99898600	Strong transcription	Primary T cells from cord blood	blood
47	chr5:99897000-99902200	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr5:99897000-99902400	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr5:99897000-99928800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr5:99897200-99898800	Weak transcription	Brain Hippocampus Middle	brain

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