Variant report

Variant	rs17238192
Chromosome Location	chr15:55514946-55514947
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:55514943..55517401-chr15:55527045..55529673,2	K562	blood:
2	chr15:55513816..55516260-chr15:55529829..55531685,2	K562	blood:
3	chr15:55512853..55516000-chr15:55580346..55583057,3	K562	blood:
4	chr15:55504661..55507549-chr15:55511770..55516084,4	K562	blood:
5	chr15:55508422..55515195-chr15:55580692..55586566,10	MCF-7	breast:
6	chr15:55514268..55516537-chr15:55573502..55575651,2	K562	blood:
7	chr15:55511874..55516207-chr15:55570260..55572623,4	K562	blood:

Variant related genes	Relation type
ENSG00000069974	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12439264	0.82[AMR][1000 genomes]
rs12440497	0.82[AMR][1000 genomes]
rs12441258	0.83[AMR][1000 genomes]
rs12441307	0.82[AMR][1000 genomes]
rs12442180	0.82[AMR][1000 genomes]
rs12442920	0.82[AMR][1000 genomes]
rs12442937	0.82[AMR][1000 genomes]
rs16976187	1.00[JPT][hapmap]
rs17238178	0.88[MEX][hapmap];0.82[AMR][1000 genomes]
rs17238199	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17238206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17819000	0.88[MEX][hapmap];0.82[AMR][1000 genomes]
rs17819012	0.88[MEX][hapmap];0.82[AMR][1000 genomes]
rs17819024	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17819036	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2899583	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55489800-55540200	Weak transcription	Esophagus	oesophagus
2	chr15:55490000-55517200	Weak transcription	Aorta	Aorta
3	chr15:55490000-55529400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr15:55490000-55562800	Weak transcription	Ovary	ovary
5	chr15:55497800-55518400	Weak transcription	Gastric	stomach
6	chr15:55508400-55517000	Weak transcription	Fetal Heart	heart
7	chr15:55508600-55522600	Weak transcription	Colon Smooth Muscle	Colon
8	chr15:55509400-55541600	Weak transcription	Small Intestine	intestine
9	chr15:55510400-55517200	Weak transcription	Fetal Muscle Leg	muscle
10	chr15:55510400-55522600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
11	chr15:55510400-55525000	Weak transcription	Fetal Muscle Trunk	muscle
12	chr15:55510400-55528000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr15:55510600-55523800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr15:55510800-55521000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:55511200-55516200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr15:55512000-55515400	Enhancers	Fetal Lung	lung
17	chr15:55512400-55516000	Strong transcription	Fetal Stomach	stomach
18	chr15:55512600-55515400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
19	chr15:55512600-55515800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr15:55512800-55515200	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr15:55512800-55515600	Flanking Active TSS	Primary B cells from cord blood	blood
22	chr15:55512800-55541600	Weak transcription	Colonic Mucosa	Colon
23	chr15:55513000-55515000	Enhancers	Primary B cells from peripheral blood	blood
24	chr15:55513000-55515800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr15:55513000-55516200	Genic enhancers	Stomach Mucosa	stomach
26	chr15:55513000-55518000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr15:55513000-55518200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
28	chr15:55513000-55518200	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr15:55513200-55515000	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr15:55513200-55515400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr15:55513200-55515400	Enhancers	Placenta	Placenta
32	chr15:55513200-55515400	Enhancers	Thymus	Thymus
33	chr15:55513200-55515600	Enhancers	Fetal Thymus	thymus
34	chr15:55513200-55515800	Enhancers	Primary T cells fromperipheralblood	blood
35	chr15:55513200-55517800	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr15:55513200-55518200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr15:55513400-55515400	Genic enhancers	K562	blood
38	chr15:55513400-55515600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
39	chr15:55513400-55517800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr15:55513400-55532400	Weak transcription	Left Ventricle	heart
41	chr15:55513600-55517800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr15:55514000-55515000	Enhancers	iPS-15b Cell Line	embryonic stem cell
43	chr15:55514000-55515600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
44	chr15:55514000-55516000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr15:55514000-55516400	Enhancers	Primary monocytes fromperipheralblood	blood
46	chr15:55514000-55516800	Strong transcription	Liver	Liver
47	chr15:55514000-55518600	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr15:55514200-55515200	Enhancers	iPS-20b Cell Line	embryonic stem cell
49	chr15:55514200-55515400	Flanking Active TSS	Primary T cells from cord blood	blood
50	chr15:55514200-55515600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood

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