Variant report

Variant	rs2189837
Chromosome Location	chr7:39759814-39759815
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:39630501..39633434-chr7:39759020..39762831,5	K562	blood:
2	chr7:39697844..39699829-chr7:39759514..39761645,2	K562	blood:
3	chr7:39756211..39760526-chr7:39771705..39775079,3	MCF-7	breast:
4	chr7:39747835..39755058-chr7:39757872..39764388,13	K562	blood:
5	chr7:39604950..39606844-chr7:39757464..39760042,2	K562	blood:
6	chr7:39660254..39665233-chr7:39756811..39764394,13	K562	blood:
7	chr7:39759344..39763475-chr7:39764953..39775706,19	K562	blood:
8	chr7:39745397..39755065-chr7:39757582..39762895,14	K562	blood:

No data

Variant related genes	Relation type
ENSG00000188185	Chromatin interaction
ENSG00000006451	Chromatin interaction
ENSG00000227172	Chromatin interaction
ENSG00000241127	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11769865	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11982634	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2107710	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2158548	0.89[EUR][1000 genomes]
rs2158549	0.93[EUR][1000 genomes]
rs2237499	0.82[ASN][1000 genomes]
rs2329464	0.93[EUR][1000 genomes]
rs2876862	0.89[EUR][1000 genomes]
rs3823742	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4723887	0.89[EUR][1000 genomes]
rs4723891	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723892	0.93[EUR][1000 genomes]
rs6462936	0.83[EUR][1000 genomes]
rs6462937	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6952363	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6952866	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6956681	0.93[EUR][1000 genomes]
rs6961667	0.89[EUR][1000 genomes]
rs6969070	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6969523	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7785049	0.89[EUR][1000 genomes]
rs7806651	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs917077	0.88[EUR][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	nsv508451	chr7:39660784-39787222	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv427777	chr7:39726513-39936904	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2189837	LINC00265	cis	Thyroid	GTEx
rs2189837	LINC00265	cis	lung	GTEx

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39755600-39760000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr7:39758600-39761000	Enhancers	iPS-20b Cell Line	embryonic stem cell
3	chr7:39758600-39761200	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr7:39758600-39761400	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr7:39758800-39760800	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr7:39759000-39760000	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr7:39759200-39760400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr7:39759200-39760800	Enhancers	Fetal Kidney	kidney
9	chr7:39759200-39761200	Enhancers	H1 Cell Line	embryonic stem cell
10	chr7:39759200-39761200	Enhancers	Fetal Intestine Large	intestine
11	chr7:39759400-39761200	Enhancers	Stomach Mucosa	stomach
12	chr7:39759400-39761800	Enhancers	Placenta	Placenta
13	chr7:39759600-39761000	Enhancers	HMEC	breast
14	chr7:39759600-39761200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr7:39759600-39761200	Enhancers	Colonic Mucosa	Colon
16	chr7:39759800-39760000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr7:39759800-39760000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr7:39759800-39760000	Enhancers	Duodenum Mucosa	Duodenum
19	chr7:39759800-39760000	Enhancers	HepG2	liver
20	chr7:39759800-39760000	Enhancers	K562	blood
21	chr7:39759800-39760000	Enhancers	NHEK	skin
22	chr7:39759800-39760200	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
23	chr7:39759800-39760200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr7:39759800-39760200	Enhancers	Esophagus	oesophagus
25	chr7:39759800-39760200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
26	chr7:39759800-39760400	Enhancers	Lung	lung
27	chr7:39759800-39760400	Enhancers	Pancreas	Pancrea
28	chr7:39759800-39761000	Enhancers	HSMM	muscle
29	chr7:39759800-39761200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr7:39759800-39761200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr7:39759800-39761200	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr7:39759800-39761200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr7:39759800-39761200	Enhancers	Fetal Intestine Small	intestine
34	chr7:39759800-39761200	Enhancers	Placenta Amnion	Placenta Amnion
35	chr7:39759800-39761200	Enhancers	Sigmoid Colon	Sigmoid Colon

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