Variant report

Variant	rs7171897
Chromosome Location	chr15:55542099-55542100
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TBL1XR1	chr15:55542073-55542169	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr15:55536038..55538706-chr15:55541637..55544470,3	K562	blood:
2	chr15:55538333..55540219-chr15:55542009..55544600,2	MCF-7	breast:
3	chr15:55540071..55542542-chr15:55580150..55582152,2	K562	blood:
4	chr15:55539059..55540962-chr15:55541694..55543566,2	K562	blood:
5	chr15:55487577..55489204-chr15:55541881..55543410,2	MCF-7	breast:

No data

Variant related genes	Relation type
RAB27A	TF binding region
ENSG00000137876	Chromatin interaction
ENSG00000069974	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10518805	1.00[CEU][hapmap]
rs12324754	0.81[EUR][1000 genomes]
rs12324775	0.81[EUR][1000 genomes]
rs12439213	1.00[CEU][hapmap]
rs12439890	1.00[CEU][hapmap]
rs12440497	1.00[CEU][hapmap]
rs12440550	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs12441258	1.00[CEU][hapmap]
rs12442937	1.00[CEU][hapmap]
rs16976218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976220	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976227	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976229	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16976231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17238178	1.00[CEU][hapmap]
rs17238220	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17819000	1.00[CEU][hapmap]
rs17819012	1.00[CEU][hapmap]
rs28499877	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28705006	0.90[EUR][1000 genomes]
rs557254	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7170936	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7171029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7177930	1.00[CEU][hapmap]
rs8039254	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9920531	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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
6	nsv1049977	chr15:55502508-55555694	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1036924	chr15:55527874-55616480	Flanking Active TSS Enhancers Weak transcription 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	17 gene(s)	inside rSNPs	diseases
8	nsv1051046	chr15:55529291-55821973	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
9	nsv569522	chr15:55532211-55611126	Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv904241	chr15:55534342-55611126	Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55490000-55562800	Weak transcription	Ovary	ovary
2	chr15:55514200-55545200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr15:55514600-55542600	Weak transcription	Hela-S3	cervix
4	chr15:55514600-55543200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr15:55514800-55560400	Weak transcription	Spleen	Spleen
6	chr15:55516000-55559600	Weak transcription	Fetal Stomach	stomach
7	chr15:55517600-55542800	Weak transcription	Thymus	Thymus
8	chr15:55517800-55542200	Weak transcription	Fetal Thymus	thymus
9	chr15:55517800-55542800	Weak transcription	Primary B cells from peripheral blood	blood
10	chr15:55520800-55574800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr15:55522800-55543200	Weak transcription	Pancreas	Pancrea
12	chr15:55522800-55547000	Weak transcription	GM12878-XiMat	blood
13	chr15:55523200-55542600	Weak transcription	HMEC	breast
14	chr15:55526800-55543200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr15:55527000-55542400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr15:55527000-55544200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr15:55527200-55542800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr15:55533800-55543400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr15:55534400-55545600	Weak transcription	Osteobl	bone
20	chr15:55534600-55542200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr15:55535000-55542200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr15:55537200-55543200	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr15:55538000-55542400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr15:55538000-55542600	Weak transcription	NHEK	skin
25	chr15:55538000-55542800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr15:55538600-55544200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr15:55538600-55549000	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr15:55538800-55544600	Genic enhancers	K562	blood
29	chr15:55539000-55543800	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr15:55539000-55544600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
31	chr15:55539400-55544600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr15:55539600-55544400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr15:55539800-55545000	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr15:55540000-55544400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr15:55540400-55542400	Enhancers	Fetal Intestine Small	intestine
36	chr15:55540400-55542600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr15:55540600-55542400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr15:55540600-55545000	Enhancers	Liver	Liver
39	chr15:55540600-55561200	Weak transcription	Esophagus	oesophagus
40	chr15:55540800-55542200	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr15:55540800-55542600	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr15:55540800-55543600	Enhancers	Fetal Lung	lung
43	chr15:55541000-55544200	Enhancers	Placenta	Placenta
44	chr15:55541200-55542200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr15:55541200-55542400	Strong transcription	Aorta	Aorta
46	chr15:55541200-55542800	Enhancers	Duodenum Mucosa	Duodenum
47	chr15:55541200-55549000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr15:55541400-55542600	Enhancers	Fetal Intestine Large	intestine
49	chr15:55541400-55542800	Weak transcription	NHLF	lung
50	chr15:55541400-55543400	Enhancers	HepG2	liver

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