Variant report

Variant	rs13020845
Chromosome Location	chr2:181987553-181987554
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:181987552-181987602	HAEpiC	amniotic membrane:	n/a
2	chr2:181987552-181987602	ECC-1	luminal epithelium:	n/a
3	chr2:181987552-181987602	PANC-1	pancreas:	n/a
4	chr2:181987552-181987602	HCPEpiC	choroid plexus:	n/a
5	chr2:181987552-181987602	HRE	kidney:	n/a
6	chr2:181987552-181987602	ovcar-3	ovarian:	n/a
7	chr2:181987552-181987602	Hela-S3	cervix:	n/a
8	chr2:181987552-181987602	T-47D	breast:	n/a
9	chr2:181987552-181987602	AG09319	gingival:	n/a
10	chr2:181987552-181987602	GM06990	blood:	n/a
11	chr2:181987552-181987602	HCT-116	colon:	n/a
12	chr2:181987552-181987602	GM12892	blood:	n/a
13	chr2:181987552-181987602	HCF	heart:	n/a
14	chr2:181987552-181987602	GM12891	blood:	n/a
15	chr2:181987552-181987602	AG10803	skin:	n/a
16	chr2:181987552-181987602	AG09309	skin:	n/a
17	chr2:181987552-181987602	AoSMC	blood vessel:	n/a
18	chr2:181987552-181987602	Jurkat	blood:	n/a
19	chr2:181987552-181987602	NB4	blood:	n/a
20	chr2:181987552-181987602	BJ	skin:	n/a
21	chr2:181987552-181987602	AG04450	lung:	fetal
22	chr2:181987552-181987602	H1-hESC	embryonic stem cell:	embryo
23	chr2:181987552-181987602	NT2-D1	testis:	n/a
24	chr2:181987552-181987602	HMEC	breast:	n/a
25	chr2:181987552-181987602	HPAEpiC	pulmonary alveolar:	n/a
26	chr2:181987552-181987602	AG04449	skin:	fetal
27	chr2:181987552-181987602	U87	brain:	n/a
28	chr2:181987552-181987602	RPTEC	kidney:	n/a
29	chr2:181987552-181987602	Hepatocyte	liver:	n/a
30	chr2:181987552-181987602	SK-N-SH_RA	brain:	n/a
31	chr2:181987552-181987602	HEK293	kidney:	embryo
32	chr2:181987552-181987602	HIPEpiC	eye:	n/a
33	chr2:181987552-181987602	SK-N-MC	brain:	n/a
34	chr2:181987552-181987602	HCM	heart:	n/a
35	chr2:181987552-181987602	GM19239	blood:	n/a
36	chr2:181987552-181987602	PFSK-1	brain:	n/a
37	chr2:181987552-181987602	Caco-2	colon:	n/a
38	chr2:181987552-181987602	NH-A	brain:	n/a
39	chr2:181987552-181987602	HRPEpiC	eye:	n/a
40	chr2:181987552-181987602	ProgFib	skin:	n/a
41	chr2:181987552-181987602	HEEpiC	esophagus:	n/a
42	chr2:181987552-181987602	GM12878	blood:	n/a
43	chr2:181987552-181987602	IMR90	lung:	fetal
44	chr2:181987552-181987602	SK-N-SH	brain:	n/a
45	chr2:181987552-181987602	SKMC	muscle:	n/a
46	chr2:181987552-181987602	PrEC	prostate:	n/a
47	chr2:181987552-181987602	HRCEpiC	kidney:	n/a
48	chr2:181987552-181987602	MCF-7	breast:	n/a
49	chr2:181987552-181987602	HNPCEpiC	eye:	n/a
50	chr2:181987552-181987602	A549	lung:	n/a

No data

Variant related genes	Relation type
ENSG00000234663	CpG island

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10171108	0.85[JPT][hapmap]
rs10171998	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs10187842	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs10930950	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs11688120	0.84[EUR][1000 genomes]
rs11891215	0.96[ASN][1000 genomes]
rs11893772	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12621277	0.82[JPT][hapmap]
rs13011738	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13011751	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13012524	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13026070	0.88[EUR][1000 genomes]
rs13029368	0.85[JPT][hapmap]
rs13031518	0.88[EUR][1000 genomes]
rs34504038	0.88[EUR][1000 genomes]
rs34601234	0.96[ASN][1000 genomes]
rs34825850	0.84[EUR][1000 genomes]
rs35049898	0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs35076700	0.84[EUR][1000 genomes]
rs35482602	0.83[EUR][1000 genomes]
rs35725888	0.84[EUR][1000 genomes]
rs4346343	0.82[CHB][hapmap]
rs4366861	0.82[CHB][hapmap];0.86[MEX][hapmap]
rs4510177	0.82[CHB][hapmap]
rs4595925	0.82[CHB][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap]
rs4667005	0.86[MEX][hapmap]
rs4990275	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs55664819	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs62178846	0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6433878	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs6433879	0.82[CHB][hapmap]
rs6433883	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs6433892	0.82[CHB][hapmap];0.81[YRI][hapmap];0.90[ASN][1000 genomes]
rs6704750	0.82[CHB][hapmap]
rs6706397	0.97[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.85[YRI][hapmap];0.93[ASN][1000 genomes]
rs6706696	0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6710650	0.83[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6711938	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs6744130	0.82[CHB][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap]
rs6745190	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs72887083	0.84[EUR][1000 genomes]
rs7371639	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs7559803	0.85[JPT][hapmap];0.86[MEX][hapmap]
rs7566146	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7566256	0.91[ASN][1000 genomes]
rs7566434	0.96[ASN][1000 genomes]
rs7569991	0.85[ASW][hapmap];0.83[CEU][hapmap];0.82[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7580796	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs7592486	0.93[ASN][1000 genomes]
rs9808318	0.82[CHB][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431824	chr2:181946115-182118559	ZNF genes & repeats Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv1005870	chr2:181968637-182921439	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv536063	chr2:181968637-182921439	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	nsv459954	chr2:181975252-182040293	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv583910	chr2:181975252-182040293	ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv3431632	chr2:181987257-181989255	Enhancers Active TSS Weak transcription Flanking Active TSS	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:181981400-181988600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:181983600-181988400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:181984800-181988200	Enhancers	Primary T cells from cord blood	blood
4	chr2:181985000-181988400	Enhancers	Primary T helper cells PMA-I stimulated	--
5	chr2:181985000-181988800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr2:181985000-181990200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:181985200-181987800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr2:181985200-181988000	Enhancers	Primary T helper naive cells from peripheral blood	blood
9	chr2:181985600-181988400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:181985800-181988400	Weak transcription	HMEC	breast
11	chr2:181985800-181988400	Weak transcription	NH-A	brain
12	chr2:181986000-181988200	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr2:181986200-181988400	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr2:181986400-181988600	Weak transcription	HSMM	muscle
15	chr2:181986600-181989000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr2:181986800-181987600	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr2:181986800-181988400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr2:181987000-181988600	Weak transcription	HSMMtube	muscle
19	chr2:181987000-181988800	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr2:181987200-181988000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr2:181987400-181988400	Enhancers	Dnd41	blood
22	chr2:181987400-181989000	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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