Variant report

Variant	rs10172216
Chromosome Location	chr2:62869546-62869547
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:62868727..62871605-chr2:62931209..62933790,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115504	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10174703	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10177638	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10179232	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10496099	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11125941	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11893614	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13397831	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13423306	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1386399	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1487074	0.89[ASN][1000 genomes]
rs1527959	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1534418	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1534419	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1534420	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1830260	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1843779	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1872789	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1872790	0.88[ASN][1000 genomes]
rs1997246	0.88[AFR][1000 genomes]
rs2129509	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2204655	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2204656	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2421713	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28814605	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2901516	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4449117	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4479415	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545965	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545966	0.90[ASN][1000 genomes]
rs6545967	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6545968	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6545969	0.89[ASN][1000 genomes]
rs6705835	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6706506	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6727888	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6749020	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6752010	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6757128	0.89[ASN][1000 genomes]
rs7349258	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7420881	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7421841	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9678363	0.84[ASN][1000 genomes]
rs974344	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs974345	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[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:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:62867800-62869800	Enhancers	Fetal Intestine Large	intestine
2	chr2:62867800-62870400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr2:62867800-62870600	Enhancers	Fetal Kidney	kidney
4	chr2:62867800-62871200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr2:62867800-62871400	Enhancers	Liver	Liver
6	chr2:62868400-62869800	Flanking Active TSS	A549	lung
7	chr2:62868400-62870400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr2:62868400-62870400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr2:62868400-62870800	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr2:62868600-62869600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:62868600-62869800	Enhancers	Duodenum Smooth Muscle	Duodenum
12	chr2:62868600-62870000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:62868600-62870200	Enhancers	Pancreatic Islets	Pancreatic Islet
14	chr2:62868600-62870400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr2:62868600-62870600	Enhancers	Fetal Lung	lung
16	chr2:62868600-62871200	Enhancers	Rectal Smooth Muscle	rectum
17	chr2:62868800-62869600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr2:62868800-62870200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr2:62868800-62870200	Enhancers	NHEK	skin
20	chr2:62868800-62870600	Enhancers	Colon Smooth Muscle	Colon
21	chr2:62869000-62870200	Weak transcription	Small Intestine	intestine
22	chr2:62869000-62870400	Enhancers	Fetal Stomach	stomach
23	chr2:62869000-62870600	Enhancers	Ovary	ovary
24	chr2:62869400-62870200	Flanking Active TSS	HepG2	liver
25	chr2:62869400-62870400	Weak transcription	Stomach Smooth Muscle	stomach

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