Variant report

Variant	rs12898521
Chromosome Location	chr15:57023826-57023827
allele	A/G
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:56989844..56991696-chr15:57023629..57025525,2	MCF-7	breast:
2	chr15:57022824..57025649-chr15:57612283..57614634,3	K562	blood:
3	chr15:57023111..57027218-chr15:57209095..57213054,4	K562	blood:
4	chr15:57022824..57027100-chr15:57611258..57614634,3	K562	blood:
5	chr15:56993897..56995437-chr15:57022399..57024475,2	K562	blood:
6	chr15:57022349..57024643-chr15:57034116..57035934,2	K562	blood:
7	chr15:57021470..57024723-chr15:57024853..57027079,3	K562	blood:
8	chr15:57023339..57026885-chr15:57210242..57212303,3	MCF-7	breast:
9	chr15:57006002..57008817-chr15:57023119..57025487,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000140262	Chromatin interaction
ENSG00000137871	Chromatin interaction
ENSG00000260172	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1010700	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10518870	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs11071287	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11071293	0.83[EUR][1000 genomes]
rs11630168	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs11632471	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11633363	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11635333	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11638497	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11638580	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11638707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11856558	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap]
rs11857706	0.93[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap]
rs12438709	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12442018	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12442189	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs12591502	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.81[EUR][1000 genomes]
rs12592389	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs12593286	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12595822	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12898760	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12900045	0.83[EUR][1000 genomes]
rs12900244	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12900441	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12901887	0.83[CEU][hapmap]
rs12903283	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12903336	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs12903862	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12905514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12906591	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12906830	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12908806	0.83[EUR][1000 genomes]
rs12910403	0.81[EUR][1000 genomes]
rs12910442	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12910459	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs12911191	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12911381	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs12912666	0.96[CEU][hapmap];0.80[CHB][hapmap];0.87[EUR][1000 genomes]
rs12913361	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12913871	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12913960	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12915816	0.83[EUR][1000 genomes]
rs12916079	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1424694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1477475	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16977020	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs17238845	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs1812395	0.83[EUR][1000 genomes]
rs1895640	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1979467	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1994081	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs2052640	0.86[EUR][1000 genomes]
rs2161934	0.86[EUR][1000 genomes]
rs2170459	0.89[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs2170463	0.88[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs2279298	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2279299	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2414480	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28620278	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs3803457	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs3816752	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3929265	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4601984	0.81[EUR][1000 genomes]
rs4774244	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4774886	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4774892	0.82[AMR][1000 genomes]
rs521904	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs538382	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs553421	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs559736	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57387969	0.89[EUR][1000 genomes]
rs62022931	0.91[EUR][1000 genomes]
rs62022933	0.90[EUR][1000 genomes]
rs62022934	0.91[EUR][1000 genomes]
rs62022954	0.80[EUR][1000 genomes]
rs6493885	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7162317	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7165831	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7168178	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7169454	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs795032	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8025391	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8036217	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8041540	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8043223	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

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	esv3422474	chr15:56867190-57244330	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv569576	chr15:57012816-57126917	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56993000-57024000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr15:57009400-57024400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr15:57011600-57024400	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr15:57011600-57024400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:57011800-57024000	Weak transcription	Aorta	Aorta
6	chr15:57012400-57025000	Weak transcription	Spleen	Spleen
7	chr15:57013400-57024200	Weak transcription	Ovary	ovary
8	chr15:57020800-57024400	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr15:57021200-57024000	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr15:57021200-57024000	Enhancers	Brain Substantia Nigra	brain
11	chr15:57021200-57024200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr15:57021400-57024200	Enhancers	Adipose Nuclei	Adipose
13	chr15:57021400-57024200	Enhancers	Brain Hippocampus Middle	brain
14	chr15:57021800-57024200	Enhancers	Fetal Lung	lung
15	chr15:57021800-57024200	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr15:57022200-57024000	Enhancers	Muscle Satellite Cultured Cells	--
17	chr15:57022200-57024000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr15:57022400-57024200	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr15:57022400-57024400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr15:57022600-57024000	Enhancers	Liver	Liver
21	chr15:57022600-57024000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr15:57022600-57024000	Enhancers	Fetal Intestine Small	intestine
23	chr15:57022600-57024000	Genic enhancers	Fetal Muscle Leg	muscle
24	chr15:57022600-57024000	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr15:57022600-57024000	Transcr. at gene 5' and 3'	Dnd41	blood
26	chr15:57022600-57024000	Enhancers	Hela-S3	cervix
27	chr15:57022600-57024000	Enhancers	NHEK	skin
28	chr15:57022600-57024200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr15:57022600-57024200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr15:57022600-57024200	Enhancers	Fetal Heart	heart
31	chr15:57022600-57024400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr15:57022600-57024400	Enhancers	Primary B cells from peripheral blood	blood
33	chr15:57022600-57024400	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr15:57022600-57024400	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr15:57022600-57024400	Enhancers	Stomach Mucosa	stomach
36	chr15:57022600-57024600	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr15:57022800-57024000	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr15:57022800-57024000	Enhancers	Right Atrium	heart
39	chr15:57022800-57024200	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr15:57022800-57024200	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr15:57022800-57024400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr15:57022800-57024400	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr15:57022800-57024600	Enhancers	Placenta	Placenta
44	chr15:57022800-57024800	Enhancers	Small Intestine	intestine
45	chr15:57023000-57024000	Enhancers	Brain Anterior Caudate	brain
46	chr15:57023000-57024000	Enhancers	Duodenum Mucosa	Duodenum
47	chr15:57023000-57024000	Enhancers	Fetal Intestine Large	intestine
48	chr15:57023000-57024000	Weak transcription	HMEC	breast
49	chr15:57023000-57024000	Weak transcription	HSMMtube	muscle
50	chr15:57023000-57024200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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