Variant report

Variant	rs1872788
Chromosome Location	chr2:62817678-62817679
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:62815568..62818395-chr2:62989644..62992050,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TMEM17-2	chr2:62817390-62817712	XLOC_002117
2	lnc-TMEM17-2	chr2:62817636-62817712	XLOC_002117
3	lnc-TMEM17-2	chr2:62817636-62817712	NONHSAT071022
4	lnc-EHBP1-2	chr2:62817389-62817712	NONHSAT071024

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1014119	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10183859	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10208675	0.81[CEU][hapmap]
rs1021268	0.84[ASN][1000 genomes]
rs10221574	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12691187	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12713463	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12713465	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13386935	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13396557	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13422188	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1527965	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1527966	0.93[ASN][1000 genomes]
rs1527967	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1534418	0.82[MKK][hapmap];1.00[YRI][hapmap]
rs1534419	0.93[YRI][hapmap]
rs1601674	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1872789	0.94[YRI][hapmap]
rs1906200	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1906201	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1906202	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2204655	0.94[YRI][hapmap]
rs4271755	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4502392	0.84[EUR][1000 genomes]
rs4671429	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4671432	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6545968	1.00[YRI][hapmap]
rs6705835	0.94[YRI][hapmap]
rs6753844	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6760804	0.80[CEU][hapmap]
rs7603495	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs901530	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9309344	0.81[ASN][1000 genomes]
rs9636442	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9677313	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv535766	chr2:62177655-62929746	Bivalent/Poised TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv916190	chr2:62233785-63006200	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv932487	chr2:62258290-63006200	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv535767	chr2:62461582-63413596	Bivalent Enhancer Strong transcription Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv834226	chr2:62745027-62894013	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv874232	chr2:62758044-62906084	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv834237	chr2:62762743-62926036	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:62798600-62818400	Weak transcription	Esophagus	oesophagus
2	chr2:62813400-62819400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr2:62813600-62819200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr2:62814200-62818000	Enhancers	HepG2	liver
5	chr2:62814600-62818400	Enhancers	Brain Substantia Nigra	brain
6	chr2:62814800-62817800	Enhancers	Brain Cingulate Gyrus	brain
7	chr2:62815000-62822600	Weak transcription	NHLF	lung
8	chr2:62815200-62822400	Weak transcription	Fetal Stomach	stomach
9	chr2:62815200-62822600	Weak transcription	NH-A	brain
10	chr2:62815400-62823000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:62815600-62818000	Enhancers	Ovary	ovary
12	chr2:62816200-62817800	Enhancers	Brain Hippocampus Middle	brain
13	chr2:62816400-62818400	Enhancers	Rectal Smooth Muscle	rectum
14	chr2:62817000-62818400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr2:62817200-62818000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr2:62817200-62819200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr2:62817400-62818800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr2:62817400-62822400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr2:62817400-62822400	Weak transcription	Osteobl	bone
20	chr2:62817600-62818000	Enhancers	Duodenum Smooth Muscle	Duodenum
21	chr2:62817600-62820800	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr2:62817600-62822000	Weak transcription	NHDF-Ad	bronchial
23	chr2:62817600-62822400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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