Variant report

Variant	rs4886409
Chromosome Location	chr15:75087879-75087880
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:75087475-75087937	GM12878	blood:	n/a	n/a
2	POLR2A	chr15:75086144-75088068	GM12892	blood:	n/a	n/a
3	POLR2A	chr15:75087797-75088061	K562	blood:	n/a	n/a
4	POLR2A	chr15:75087766-75088162	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:75085754..75088425-chr15:75092010..75094083,2	MCF-7	breast:
2	chr15:75086825..75088455-chr15:75228653..75231420,2	K562	blood:

Variant related genes	Relation type
CSK	TF binding region
ENSG00000103653	Chromatin interaction
ENSG00000178741	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12438333	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs12439525	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439944	0.80[AMR][1000 genomes]
rs12441444	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12443172	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12594158	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1531162	1.00[CEU][hapmap];0.81[GIH][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap]
rs1531163	1.00[CEU][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap]
rs16972714	0.86[AMR][1000 genomes]
rs2229730	0.84[ASW][hapmap];1.00[CEU][hapmap];0.81[GIH][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2305667	0.82[CEU][hapmap]
rs28397782	1.00[CEU][hapmap];0.81[GIH][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28431073	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28577988	0.86[AMR][1000 genomes]
rs28583379	0.80[AMR][1000 genomes]
rs2899827	1.00[CEU][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3743486	0.84[ASW][hapmap];1.00[CEU][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3743487	1.00[CEU][hapmap];0.81[TSI][hapmap]
rs3803568	0.84[ASW][hapmap];1.00[CEU][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4886620	1.00[CEU][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4886627	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7165811	1.00[CEU][hapmap]
rs8039046	1.00[CEU][hapmap];0.81[GIH][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs9796628	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]

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	nsv904380	chr15:74869438-75142761	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv833055	chr15:74988344-75166288	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75077800-75092000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr15:75079400-75093800	Weak transcription	Aorta	Aorta
3	chr15:75080800-75088600	Enhancers	Stomach Mucosa	stomach
4	chr15:75081200-75091400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr15:75081800-75092000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr15:75081800-75092000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr15:75082200-75092200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr15:75082400-75088000	Genic enhancers	Fetal Intestine Small	intestine
9	chr15:75082400-75098400	Weak transcription	Fetal Kidney	kidney
10	chr15:75082600-75088400	Genic enhancers	Fetal Thymus	thymus
11	chr15:75082600-75090400	Weak transcription	HepG2	liver
12	chr15:75082600-75093200	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr15:75083000-75089800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr15:75083000-75090400	Weak transcription	Dnd41	blood
15	chr15:75083000-75092000	Weak transcription	Hela-S3	cervix
16	chr15:75083000-75093000	Weak transcription	HUVEC	blood vessel
17	chr15:75083200-75090400	Weak transcription	Fetal Brain Female	brain
18	chr15:75083200-75091800	Weak transcription	A549	lung
19	chr15:75083200-75092400	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
20	chr15:75083200-75093600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr15:75083400-75090600	Weak transcription	Fetal Lung	lung
22	chr15:75083800-75091600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr15:75084400-75088000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr15:75084400-75093200	Genic enhancers	Primary B cells from cord blood	blood
25	chr15:75084400-75094600	Weak transcription	HSMMtube	muscle
26	chr15:75084800-75091000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr15:75085200-75090600	Weak transcription	Psoas Muscle	Psoas
28	chr15:75085200-75091400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr15:75085400-75088200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr15:75085600-75091800	Weak transcription	NHDF-Ad	bronchial
31	chr15:75085800-75088400	Weak transcription	Fetal Muscle Leg	muscle
32	chr15:75085800-75088600	Enhancers	NHEK	skin
33	chr15:75085800-75089200	Enhancers	Duodenum Mucosa	Duodenum
34	chr15:75085800-75090200	Weak transcription	Stomach Smooth Muscle	stomach
35	chr15:75085800-75091800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr15:75085800-75091800	Weak transcription	Colon Smooth Muscle	Colon
37	chr15:75085800-75093200	Weak transcription	Ovary	ovary
38	chr15:75086000-75088400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr15:75086000-75089200	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr15:75086000-75090000	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr15:75086000-75090200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr15:75086000-75090200	Weak transcription	Colonic Mucosa	Colon
43	chr15:75086000-75090200	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr15:75086000-75090400	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr15:75086000-75090400	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr15:75086000-75090400	Weak transcription	Rectal Smooth Muscle	rectum
47	chr15:75086000-75090600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr15:75086000-75090600	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr15:75086000-75090600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr15:75086000-75090800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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