Variant report

Variant	rs12900028
Chromosome Location	chr15:74666027-74666028
allele	C/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:35)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:35 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:74666006..74666589-chr15:74835580..74836342,2	MCF-7	breast:
2	chr15:74665429..74667664-chr15:74747982..74750255,2	MCF-7	breast:
3	chr15:74665025..74668014-chr15:74668385..74670407,3	MCF-7	breast:
4	chr15:74664518..74667093-chr15:74731124..74732993,2	MCF-7	breast:
5	chr15:74665902..74667600-chr15:74730654..74731665,8	K562	blood:
6	chr15:74665724..74666602-chr15:74716103..74717034,2	K562	blood:
7	chr15:74664221..74666874-chr15:74684631..74687435,2	K562	blood:
8	chr15:74665952..74666781-chr15:75062636..75063591,2	MCF-7	breast:
9	chr15:74665092..74667430-chr15:74726842..74729796,2	K562	blood:
10	chr15:74664672..74667592-chr15:74837544..74840546,3	MCF-7	breast:
11	chr15:74665889..74666878-chr15:74913167..74914585,8	MCF-7	breast:
12	chr15:74665365..74667927-chr15:74780037..74785377,6	MCF-7	breast:
13	chr15:74665674..74667087-chr15:74730530..74731799,6	MCF-7	breast:
14	chr15:74665357..74666676-chr15:74923962..74924983,9	K562	blood:
15	chr15:74664841..74669022-chr15:74717731..74721779,3	K562	blood:
16	chr15:74664899..74666898-chr15:74740722..74743644,2	K562	blood:
17	chr15:74665425..74667643-chr15:74752949..74754890,2	K562	blood:
18	chr15:74665745..74666851-chr15:74913129..74914141,6	MCF-7	breast:
19	chr15:74665680..74666890-chr15:75060904..75061896,5	K562	blood:
20	chr15:74665568..74668523-chr15:74922376..74925547,4	MCF-7	breast:
21	chr15:74665664..74666620-chr15:75092571..75093078,2	K562	blood:
22	chr15:74665982..74668403-chr15:74893258..74895614,2	MCF-7	breast:
23	chr15:74664422..74666409-chr15:74928814..74930536,2	MCF-7	breast:
24	chr15:74665122..74667877-chr15:74906569..74911881,5	MCF-7	breast:
25	chr15:74665654..74666531-chr15:74781812..74782816,5	K562	blood:
26	chr15:74665730..74666341-chr15:74913344..74914091,2	K562	blood:
27	chr15:74665832..74668344-chr15:74734420..74737401,2	K562	blood:
28	chr15:74665953..74666593-chr15:75061227..75061819,2	MCF-7	breast:
29	chr15:74665248..74670570-chr15:74911003..74915113,6	MCF-7	breast:
30	chr15:74665453..74667821-chr15:74780445..74783665,3	MCF-7	breast:
31	chr15:74665280..74666364-chr15:74674391..74675333,6	K562	blood:
32	chr15:74664932..74669170-chr15:74905600..74910371,8	K562	blood:
33	chr15:74665255..74670127-chr15:74905870..74910808,10	MCF-7	breast:
34	chr15:74665743..74666548-chr15:74924006..74925016,4	MCF-7	breast:
35	chr15:74665619..74667467-chr17:66287023..66289875,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000247240	Chromatin interaction
ENSG00000212279	Chromatin interaction
ENSG00000108932	Chromatin interaction
ENSG00000179335	Chromatin interaction
ENSG00000103653	Chromatin interaction
ENSG00000260919	Chromatin interaction
ENSG00000260103	Chromatin interaction
ENSG00000138629	Chromatin interaction
ENSG00000141337	Chromatin interaction
ENSG00000261775	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11632698	0.92[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11635047	0.88[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs11638442	0.93[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12440952	0.81[EUR][1000 genomes]
rs12912592	0.85[EUR][1000 genomes]
rs12917295	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12917557	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1484210	0.82[CEU][hapmap]
rs1564783	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs2959011	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs34578565	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35807116	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4887134	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs4887135	0.93[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs56339065	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs900801	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428641	chr15:74555113-74724630	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	nsv482615	chr15:74593625-74757962	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
3	nsv904351	chr15:74638965-74697084	Weak transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv904352	chr15:74638965-74715205	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74658600-74666200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:74658800-74666200	Weak transcription	Right Atrium	heart
3	chr15:74659400-74666200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr15:74662200-74666200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr15:74662200-74666200	Weak transcription	Ovary	ovary
6	chr15:74665400-74666200	Enhancers	Spleen	Spleen
7	chr15:74665600-74666200	Enhancers	H1 Cell Line	embryonic stem cell
8	chr15:74665600-74666200	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr15:74665600-74666200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr15:74665600-74666200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr15:74665600-74666200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
12	chr15:74665600-74666200	Enhancers	Placenta	Placenta
13	chr15:74665600-74666400	Flanking Bivalent TSS/Enh	HepG2	liver
14	chr15:74665600-74666600	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr15:74665600-74667800	Flanking Active TSS	Hela-S3	cervix
16	chr15:74665800-74666200	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr15:74665800-74666200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr15:74665800-74666200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:74665800-74666200	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr15:74665800-74666200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr15:74665800-74666200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr15:74665800-74666200	Enhancers	Primary hematopoietic stem cells	blood
23	chr15:74665800-74666200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr15:74665800-74666200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr15:74665800-74666200	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr15:74665800-74666200	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
27	chr15:74665800-74666200	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
28	chr15:74665800-74666200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr15:74665800-74666200	Enhancers	Adipose Nuclei	Adipose
30	chr15:74665800-74666200	Enhancers	Brain Angular Gyrus	brain
31	chr15:74665800-74666200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr15:74665800-74666200	Enhancers	Brain Substantia Nigra	brain
33	chr15:74665800-74666200	Enhancers	Colon Smooth Muscle	Colon
34	chr15:74665800-74666200	Bivalent Enhancer	Fetal Intestine Small	intestine
35	chr15:74665800-74666200	Enhancers	Fetal Lung	lung
36	chr15:74665800-74666200	Bivalent Enhancer	Fetal Muscle Leg	muscle
37	chr15:74665800-74666200	Bivalent Enhancer	Fetal Stomach	stomach
38	chr15:74665800-74666200	Enhancers	Gastric	stomach
39	chr15:74665800-74666200	Enhancers	Left Ventricle	heart
40	chr15:74665800-74666200	Enhancers	Pancreas	Pancrea
41	chr15:74665800-74666200	Enhancers	Right Ventricle	heart
42	chr15:74665800-74666200	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr15:74665800-74666200	Flanking Active TSS	K562	blood
44	chr15:74665800-74667000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
45	chr15:74665800-74667200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
46	chr15:74665800-74667600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr15:74665800-74667600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr15:74665800-74667600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr15:74665800-74667800	Enhancers	Fetal Heart	heart
50	chr15:74666000-74666200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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