Variant report

Variant	rs10518804
Chromosome Location	chr15:55490726-55490727
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SETDB1	chr15:55490650-55491551	U2OS	brain:	n/a	n/a
2	CBX3	chr15:55490666-55491337	K562	blood:	n/a	n/a
3	KAP1	chr15:55490216-55492297	K562	blood:	n/a	n/a
4	SETDB1	chr15:55490329-55491659	K562	blood:	n/a	n/a
5	POLR2A	chr15:55490412-55491293	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:55489042..55491644-chr15:55640711..55643190,2	K562	blood:
2	chr15:55487872..55490645-chr15:55490710..55492637,2	K562	blood:
3	chr15:55489860..55492561-chr15:55500870..55502505,2	K562	blood:
4	chr15:55485508..55492313-chr15:55579801..55583590,12	K562	blood:
5	chr15:55490157..55491866-chr15:55610487..55612972,2	MCF-7	breast:
6	chr15:54266407..54270072-chr15:55486535..55491034,4	MCF-7	breast:

No data

Variant related genes	Relation type
RSL24D1	TF binding region
ENSG00000259669	Chromatin interaction
ENSG00000069974	Chromatin interaction
ENSG00000069943	Chromatin interaction
ENSG00000225973	Chromatin interaction
ENSG00000137876	Chromatin interaction

Extended variants
information (count: 118 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10162819	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10162843	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1050931	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1061821	0.88[ASN][1000 genomes]
rs1061822	0.93[ASN][1000 genomes]
rs1061823	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1061824	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1061870	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1061873	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1061874	0.88[ASN][1000 genomes]
rs1061875	0.88[ASN][1000 genomes]
rs11852763	0.93[ASN][1000 genomes]
rs11855907	0.93[ASN][1000 genomes]
rs11855973	0.93[ASN][1000 genomes]
rs11855978	0.90[ASN][1000 genomes]
rs11856010	0.87[ASN][1000 genomes]
rs11857087	0.85[ASN][1000 genomes]
rs12385963	0.85[ASN][1000 genomes]
rs12440420	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs13380400	0.93[ASN][1000 genomes]
rs13733	0.88[ASN][1000 genomes]
rs16976036	0.92[CHB][hapmap];0.82[ASN][1000 genomes]
rs16976039	0.93[CHB][hapmap];0.82[ASN][1000 genomes]
rs16976065	0.85[ASN][1000 genomes]
rs16976083	0.86[ASN][1000 genomes]
rs16976094	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16976116	0.83[ASN][1000 genomes]
rs16976149	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16976177	1.00[JPT][hapmap]
rs17238171	1.00[JPT][hapmap]
rs2289059	0.85[YRI][hapmap]
rs28433503	0.90[ASN][1000 genomes]
rs28449712	0.90[ASN][1000 genomes]
rs28489312	0.93[ASN][1000 genomes]
rs28493279	0.84[ASN][1000 genomes]
rs28499113	0.84[ASN][1000 genomes]
rs28508034	0.90[ASN][1000 genomes]
rs28522816	0.87[ASN][1000 genomes]
rs28526269	0.90[ASN][1000 genomes]
rs28530662	0.90[ASN][1000 genomes]
rs28535372	0.90[ASN][1000 genomes]
rs28541469	0.90[ASN][1000 genomes]
rs28558576	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28562431	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28564077	0.91[ASN][1000 genomes]
rs28589384	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs28589609	0.84[ASN][1000 genomes]
rs28590021	0.84[ASN][1000 genomes]
rs28591259	0.90[ASN][1000 genomes]
rs28592928	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28600759	0.84[ASN][1000 genomes]
rs28630909	0.90[ASN][1000 genomes]
rs28636526	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28649719	0.90[ASN][1000 genomes]
rs28673043	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28699327	0.90[ASN][1000 genomes]
rs28704109	0.93[ASN][1000 genomes]
rs28706531	0.85[ASN][1000 genomes]
rs28708989	0.90[ASN][1000 genomes]
rs28710976	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs28714578	0.93[ASN][1000 genomes]
rs28784096	0.84[ASN][1000 genomes]
rs28864456	0.84[ASN][1000 genomes]
rs28889339	0.84[ASN][1000 genomes]
rs2899580	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2899581	0.93[ASN][1000 genomes]
rs2899582	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3179664	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3759861	0.86[CHB][hapmap];0.83[ASN][1000 genomes]
rs3759862	0.88[CHB][hapmap];0.85[ASN][1000 genomes]
rs3809539	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3809540	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4238316	0.90[ASN][1000 genomes]
rs4503734	0.83[ASN][1000 genomes]
rs4545742	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4632077	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs56328329	0.84[ASN][1000 genomes]
rs62020114	0.87[ASN][1000 genomes]
rs62020115	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6493768	0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs6493769	0.87[ASN][1000 genomes]
rs6493771	0.83[ASN][1000 genomes]
rs7165491	0.90[ASN][1000 genomes]
rs7168472	0.93[CEU][hapmap];0.88[CHB][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7168737	0.90[ASN][1000 genomes]
rs7172108	0.90[ASN][1000 genomes]
rs7172289	0.90[ASN][1000 genomes]
rs7176676	0.83[ASN][1000 genomes]
rs7179365	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7180504	0.85[YRI][hapmap]
rs7180594	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7181237	0.80[CHB][hapmap];1.00[JPT][hapmap]
rs7183255	1.00[JPT][hapmap]
rs73409851	0.84[ASN][1000 genomes]
rs73409853	0.84[ASN][1000 genomes]
rs8027098	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs8027256	0.85[ASN][1000 genomes]
rs8028525	0.84[ASN][1000 genomes]
rs8030981	0.90[ASN][1000 genomes]
rs8031949	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs8033588	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8034063	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8034402	0.92[CEU][hapmap];0.86[CHB][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs8034853	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8034882	0.92[CEU][hapmap];0.93[CHB][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8035625	0.85[CEU][hapmap];0.86[CHB][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs8043029	0.86[CHB][hapmap];0.85[ASN][1000 genomes]
rs9300	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9920136	0.84[ASN][1000 genomes]
rs9920165	1.00[CEU][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9920219	0.84[ASN][1000 genomes]
rs9920220	0.84[ASN][1000 genomes]
rs9920737	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043176	chr15:55010228-55563000	Genic enhancers Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1042741	chr15:55068022-55622497	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1039471	chr15:55137606-55552555	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers 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 miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv917323	chr15:55290499-56041334	Genic enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55489600-55497600	Weak transcription	Gastric	stomach
2	chr15:55489600-55504000	Weak transcription	Spleen	Spleen
3	chr15:55489600-55513200	Weak transcription	Lung	lung
4	chr15:55489800-55499400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr15:55489800-55503400	Weak transcription	Pancreas	Pancrea
6	chr15:55489800-55540200	Weak transcription	Esophagus	oesophagus
7	chr15:55490000-55490800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr15:55490000-55491000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr15:55490000-55493800	Weak transcription	Stomach Mucosa	stomach
10	chr15:55490000-55496000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr15:55490000-55496400	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr15:55490000-55496600	Weak transcription	Liver	Liver
13	chr15:55490000-55496800	Weak transcription	Placenta	Placenta
14	chr15:55490000-55497400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr15:55490000-55497400	Weak transcription	Adipose Nuclei	Adipose
16	chr15:55490000-55497600	Weak transcription	Fetal Stomach	stomach
17	chr15:55490000-55501600	Weak transcription	Left Ventricle	heart
18	chr15:55490000-55502000	Weak transcription	Colonic Mucosa	Colon
19	chr15:55490000-55509600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr15:55490000-55510000	Weak transcription	NHLF	lung
21	chr15:55490000-55513000	Weak transcription	Fetal Intestine Large	intestine
22	chr15:55490000-55513200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr15:55490000-55513200	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr15:55490000-55513200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr15:55490000-55517200	Weak transcription	Aorta	Aorta
26	chr15:55490000-55529400	Weak transcription	Rectal Smooth Muscle	rectum
27	chr15:55490000-55562800	Weak transcription	Ovary	ovary
28	chr15:55490200-55491000	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr15:55490200-55491200	Weak transcription	Fetal Heart	heart
30	chr15:55490200-55494200	Weak transcription	HepG2	liver
31	chr15:55490200-55494400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr15:55490200-55496400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr15:55490200-55496400	Weak transcription	Stomach Smooth Muscle	stomach
34	chr15:55490200-55496600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr15:55490200-55496800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr15:55490200-55497000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr15:55490200-55497000	Weak transcription	Primary B cells from peripheral blood	blood
38	chr15:55490200-55497000	Weak transcription	Primary hematopoietic stem cells	blood
39	chr15:55490200-55497200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr15:55490200-55497200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr15:55490200-55499400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr15:55490200-55510000	Weak transcription	Fetal Kidney	kidney
43	chr15:55490200-55510200	Weak transcription	Fetal Lung	lung
44	chr15:55490200-55511400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr15:55490200-55511400	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr15:55490200-55511400	Weak transcription	Osteobl	bone
47	chr15:55490200-55513200	Weak transcription	Duodenum Mucosa	Duodenum
48	chr15:55490200-55513800	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr15:55490200-55514000	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr15:55490400-55493800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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