Variant report

Variant	rs2290335
Chromosome Location	chr15:52662670-52662671
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52659363..52660906-chr15:52661946..52664641,2	K562	blood:
2	chr15:52656876..52658459-chr15:52661016..52663662,2	MCF-7	breast:
3	chr15:52660335..52662877-chr15:52670040..52672316,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12438578	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12440929	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12441597	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12900962	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs12901814	0.82[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs1405183	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1405184	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1669877	0.81[CHB][hapmap]
rs1724630	0.82[CHB][hapmap]
rs17707852	0.87[YRI][hapmap]
rs1965563	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2290332	0.92[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];0.97[LWK][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2290336	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28533733	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs3794557	1.00[CHB][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs3794564	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3794565	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3794566	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.97[LWK][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7176600	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7176830	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8025937	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8030535	0.82[ASW][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.97[LWK][hapmap];0.88[MKK][hapmap];0.86[TSI][hapmap];0.92[YRI][hapmap];0.81[ASN][1000 genomes]
rs8032995	0.81[AFR][1000 genomes]
rs871488	0.82[ASW][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];0.86[TSI][hapmap];0.92[YRI][hapmap];0.81[ASN][1000 genomes]
rs940970	0.82[ASW][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];0.86[TSI][hapmap];0.92[YRI][hapmap];0.81[ASN][1000 genomes]

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	esv1846455	chr15:52501831-52714452	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer 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 target site	52 gene(s)	inside rSNPs	diseases
3	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv1054899	chr15:52662365-52803756	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52609800-52677600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:52611800-52675800	Weak transcription	Gastric	stomach
3	chr15:52613600-52666600	Weak transcription	Right Ventricle	heart
4	chr15:52621200-52666600	Weak transcription	Fetal Brain Male	brain
5	chr15:52630600-52684800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr15:52631600-52679200	Weak transcription	Fetal Intestine Small	intestine
7	chr15:52632600-52670400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr15:52638000-52671600	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr15:52640600-52666600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr15:52641800-52666800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr15:52644000-52664200	Weak transcription	NHLF	lung
12	chr15:52644000-52666600	Weak transcription	Fetal Muscle Trunk	muscle
13	chr15:52644200-52680800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr15:52644600-52663800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr15:52644600-52663800	Weak transcription	Spleen	Spleen
16	chr15:52644600-52665400	Weak transcription	A549	lung
17	chr15:52644600-52730200	Weak transcription	Esophagus	oesophagus
18	chr15:52646200-52663800	Weak transcription	Lung	lung
19	chr15:52647400-52690600	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr15:52649000-52687200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr15:52649600-52670600	Strong transcription	Primary T helper cells fromperipheralblood	blood
22	chr15:52649600-52677600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr15:52649800-52662800	Strong transcription	Primary B cells from peripheral blood	blood
24	chr15:52649800-52676400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr15:52650000-52670200	Strong transcription	Primary T cells fromperipheralblood	blood
26	chr15:52650000-52670400	Strong transcription	HUVEC	blood vessel
27	chr15:52650200-52669200	Strong transcription	Primary B cells from cord blood	blood
28	chr15:52650400-52666800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr15:52651000-52666600	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr15:52652200-52670400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr15:52653200-52663600	Weak transcription	Pancreas	Pancrea
32	chr15:52653400-52666600	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr15:52653400-52666800	Weak transcription	Aorta	Aorta
34	chr15:52653600-52677400	Weak transcription	Colonic Mucosa	Colon
35	chr15:52654400-52666400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr15:52654400-52666400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr15:52655000-52666600	Weak transcription	Osteobl	bone
38	chr15:52655800-52665800	Weak transcription	Fetal Thymus	thymus
39	chr15:52655800-52666400	Weak transcription	Liver	Liver
40	chr15:52655800-52675200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr15:52656200-52666600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr15:52656800-52674000	Strong transcription	Primary T cells from cord blood	blood
43	chr15:52657400-52670000	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr15:52657800-52666600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr15:52658000-52663600	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr15:52658400-52687200	Weak transcription	Small Intestine	intestine
47	chr15:52658800-52664800	Strong transcription	NHDF-Ad	bronchial
48	chr15:52658800-52666600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr15:52659000-52664400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr15:52659000-52676600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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