Variant report

Variant	rs7898820
Chromosome Location	chr10:27536132-27536133
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:27499802..27501903-chr10:27533601..27536137,2	MCF-7	breast:
2	chr10:27529615..27533136-chr10:27533477..27538101,8	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ACBD5-1	chr10:27534782-27541235	NR_003525

Variant related genes	Relation type
ENSG00000262412	Chromatin interaction
ENSG00000107897	Chromatin interaction

Extended variants
information (count: 126 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs1002351	0.89[ASN][1000 genomes]
rs10466100	0.86[ASN][1000 genomes]
rs10764681	0.81[ASN][1000 genomes]
rs10764682	0.81[ASN][1000 genomes]
rs10764687	0.81[ASN][1000 genomes]
rs10829209	0.86[ASN][1000 genomes]
rs10829214	0.89[ASN][1000 genomes]
rs10829215	0.89[ASN][1000 genomes]
rs10829216	0.89[ASN][1000 genomes]
rs11015602	0.84[ASN][1000 genomes]
rs11015607	0.86[ASN][1000 genomes]
rs11015608	0.86[ASN][1000 genomes]
rs11015609	0.86[ASN][1000 genomes]
rs11015610	0.86[ASN][1000 genomes]
rs11015611	0.86[ASN][1000 genomes]
rs11015612	0.86[ASN][1000 genomes]
rs11015614	0.89[ASN][1000 genomes]
rs11015615	0.89[ASN][1000 genomes]
rs11813084	0.86[ASN][1000 genomes]
rs11813101	0.86[ASN][1000 genomes]
rs11816764	0.86[ASN][1000 genomes]
rs11816767	0.86[ASN][1000 genomes]
rs11818136	0.86[ASN][1000 genomes]
rs12098587	0.89[ASN][1000 genomes]
rs12098618	0.89[ASN][1000 genomes]
rs12240963	0.93[ASN][1000 genomes]
rs12241350	0.86[ASN][1000 genomes]
rs12243607	0.89[ASN][1000 genomes]
rs12246088	0.86[ASN][1000 genomes]
rs12246158	0.86[ASN][1000 genomes]
rs12247183	0.86[ASN][1000 genomes]
rs12251316	0.89[ASN][1000 genomes]
rs12253696	0.82[ASN][1000 genomes]
rs12257786	0.89[ASN][1000 genomes]
rs12259138	0.86[ASN][1000 genomes]
rs12259499	0.89[ASN][1000 genomes]
rs12261094	0.89[ASN][1000 genomes]
rs12262674	0.89[ASN][1000 genomes]
rs12268796	0.82[ASN][1000 genomes]
rs1557163	0.89[ASN][1000 genomes]
rs1557164	0.89[ASN][1000 genomes]
rs1557165	0.89[ASN][1000 genomes]
rs1557166	0.89[ASN][1000 genomes]
rs16927640	0.86[ASN][1000 genomes]
rs16927646	0.89[ASN][1000 genomes]
rs2275751	1.00[EUR][1000 genomes]
rs34037342	0.86[ASN][1000 genomes]
rs34613194	0.86[ASN][1000 genomes]
rs34856168	0.86[ASN][1000 genomes]
rs36121140	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3780923	1.00[EUR][1000 genomes]
rs3818962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3818965	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3818968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3824594	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs41314978	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55872244	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55884764	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56710909	0.85[ASN][1000 genomes]
rs56787693	0.89[ASN][1000 genomes]
rs57096075	0.86[ASN][1000 genomes]
rs57470366	0.86[ASN][1000 genomes]
rs57563582	0.91[ASN][1000 genomes]
rs57704178	0.86[ASN][1000 genomes]
rs58326983	0.86[ASN][1000 genomes]
rs58649395	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs58843203	0.86[ASN][1000 genomes]
rs59116633	0.86[ASN][1000 genomes]
rs59638069	0.86[ASN][1000 genomes]
rs59935135	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59947739	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61607571	0.89[ASN][1000 genomes]
rs61686723	0.89[ASN][1000 genomes]
rs61737707	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs61737928	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs6482605	0.86[ASN][1000 genomes]
rs6482606	0.86[ASN][1000 genomes]
rs6482609	0.89[ASN][1000 genomes]
rs6482610	0.89[ASN][1000 genomes]
rs6482611	0.89[ASN][1000 genomes]
rs6482612	0.89[ASN][1000 genomes]
rs7068182	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7068463	0.86[ASN][1000 genomes]
rs7069127	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7069761	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7070377	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7070508	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7072412	0.86[ASN][1000 genomes]
rs7074120	0.86[ASN][1000 genomes]
rs7084392	0.86[ASN][1000 genomes]
rs7084515	0.86[ASN][1000 genomes]
rs7085266	0.86[ASN][1000 genomes]
rs7087198	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7090639	0.86[ASN][1000 genomes]
rs7091897	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7092591	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7092612	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7358044	0.89[ASN][1000 genomes]
rs7358057	0.89[ASN][1000 genomes]
rs74126939	0.86[ASN][1000 genomes]
rs74126942	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs74126943	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs74126946	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74126948	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7897124	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7898083	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7898338	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7900802	0.86[ASN][1000 genomes]
rs7902900	0.87[ASN][1000 genomes]
rs7903450	0.82[ASN][1000 genomes]
rs7906528	0.89[ASN][1000 genomes]
rs7907326	0.89[ASN][1000 genomes]
rs7908434	0.89[ASN][1000 genomes]
rs7909359	0.86[ASN][1000 genomes]
rs7910142	0.86[ASN][1000 genomes]
rs7912056	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7913638	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7914017	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7920178	0.81[ASN][1000 genomes]
rs7920608	0.80[ASN][1000 genomes]
rs7923708	0.86[ASN][1000 genomes]
rs7923846	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422253	chr10:27431366-27575370	Strong transcription Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3337781	chr10:27472216-27666703	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv8614	chr10:27504487-27828406	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv947786	chr10:27535141-27541912	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:27532600-27536400	Weak transcription	Fetal Muscle Leg	muscle
2	chr10:27532600-27536400	Weak transcription	Right Atrium	heart
3	chr10:27532600-27540400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr10:27532600-27541200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr10:27532600-27541200	Weak transcription	Esophagus	oesophagus
6	chr10:27532600-27541200	Weak transcription	Pancreas	Pancrea
7	chr10:27532600-27541200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr10:27532800-27536400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr10:27532800-27536400	Weak transcription	Psoas Muscle	Psoas
10	chr10:27532800-27536600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr10:27532800-27537000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr10:27532800-27541000	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr10:27532800-27541000	Weak transcription	Adipose Nuclei	Adipose
14	chr10:27532800-27541200	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr10:27532800-27541200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr10:27532800-27541200	Weak transcription	Right Ventricle	heart
17	chr10:27533000-27536400	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr10:27533000-27541000	Weak transcription	Hela-S3	cervix
19	chr10:27533000-27541200	Weak transcription	Primary T cells from cord blood	blood
20	chr10:27533000-27541200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr10:27533000-27541200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr10:27533000-27541200	Weak transcription	Brain Cingulate Gyrus	brain
23	chr10:27533000-27541200	Weak transcription	Brain Substantia Nigra	brain
24	chr10:27533000-27541200	Weak transcription	Fetal Kidney	kidney
25	chr10:27533200-27536400	Weak transcription	Fetal Heart	heart
26	chr10:27535200-27536800	Enhancers	HepG2	liver
27	chr10:27535400-27536400	Enhancers	Fetal Intestine Large	intestine
28	chr10:27535400-27537200	Enhancers	Left Ventricle	heart
29	chr10:27535800-27536200	Weak transcription	Fetal Intestine Small	intestine

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