Variant report

Variant	rs2640062
Chromosome Location	chr1:95185274-95185275
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10874885	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10874887	0.84[ASN][1000 genomes]
rs11165226	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11582204	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12406332	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1245477	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1532250	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1532251	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1532252	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2640061	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2640063	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2802097	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2802098	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2802099	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2802100	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2802101	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2802102	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2802103	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2933916	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2933917	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2997377	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2997378	0.83[ASN][1000 genomes]
rs2997379	0.83[ASN][1000 genomes]
rs2997380	0.83[ASN][1000 genomes]
rs34670167	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4847346	0.89[ASN][1000 genomes]
rs4847348	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6665058	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[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	nsv1001587	chr1:95027691-95318680	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
2	nsv871916	chr1:95143999-95189230	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1001043	chr1:95158042-95185906	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2640062	FAM69A	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:95152800-95195000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr1:95168200-95200400	Weak transcription	Pancreas	Pancrea
3	chr1:95169400-95200400	Weak transcription	Colonic Mucosa	Colon
4	chr1:95173400-95200600	Weak transcription	Right Atrium	heart
5	chr1:95174600-95186000	Weak transcription	Fetal Thymus	thymus
6	chr1:95175800-95185400	Weak transcription	Spleen	Spleen
7	chr1:95175800-95192600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr1:95175800-95193000	Weak transcription	Fetal Stomach	stomach
9	chr1:95176200-95189200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:95178200-95185800	Enhancers	Primary neutrophils fromperipheralblood	blood
11	chr1:95179600-95193800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr1:95180000-95185600	Weak transcription	Primary B cells from cord blood	blood
13	chr1:95180000-95188400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr1:95180000-95189200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr1:95180200-95185600	Weak transcription	A549	lung
16	chr1:95180200-95189000	Weak transcription	Fetal Intestine Large	intestine
17	chr1:95180200-95189600	Weak transcription	NHDF-Ad	bronchial
18	chr1:95180800-95186200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:95181400-95189400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:95181600-95186000	Weak transcription	Dnd41	blood
21	chr1:95182600-95191000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:95183000-95189200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr1:95183200-95185400	Weak transcription	Primary hematopoietic stem cells	blood
24	chr1:95184000-95188800	Strong transcription	Fetal Intestine Small	intestine
25	chr1:95184400-95190000	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr1:95184400-95190800	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr1:95184600-95185600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:95184800-95186200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:95185000-95185800	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr1:95185000-95190400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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