Variant report

Variant	rs12903587
Chromosome Location	chr15:93455471-93455472
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:93455340..93459027-chr15:93459316..93461094,3	MCF-7	breast:
2	chr15:93333327..93367027-chr15:93419774..93462750,363	K562	blood:
3	chr15:93344712..93371031-chr15:93418700..93467618,365	MCF-7	breast:
4	chr15:93361979..93363621-chr15:93454953..93456555,2	MCF-7	breast:
5	chr15:93350620..93356582-chr15:93455419..93466792,23	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258922	Chromatin interaction
ENSG00000185442	Chromatin interaction
ENSG00000258527	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10852185	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11074118	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11074119	0.82[AMR][1000 genomes]
rs1143115	0.94[ASW][hapmap];0.88[JPT][hapmap];0.92[MEX][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes]
rs12904071	0.84[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12906861	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12907473	0.84[CEU][hapmap];0.81[CHB][hapmap];0.93[JPT][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12908968	1.00[ASW][hapmap];0.84[CEU][hapmap];0.81[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1439618	0.83[ASW][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes]
rs1439619	0.82[AMR][1000 genomes]
rs17648433	0.90[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs2272461	0.81[JPT][hapmap]
rs34918115	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35813181	0.91[ASN][1000 genomes]
rs3826037	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4146836	0.81[AMR][1000 genomes]
rs4146837	0.89[ASW][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes]
rs7164173	0.84[CHD][hapmap]
rs7170052	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904499	chr15:92914795-93472582	Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	163 gene(s)	inside rSNPs	diseases
2	nsv948738	chr15:93070742-93728147	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
3	nsv1049490	chr15:93134405-93591660	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
4	nsv530846	chr15:93323949-94030462	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
5	nsv948881	chr15:93383740-93603608	Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
6	nsv1047496	chr15:93412778-93475878	Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	87 gene(s)	inside rSNPs	diseases
7	nsv1036560	chr15:93413594-93462163	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	87 gene(s)	inside rSNPs	diseases
8	nsv530847	chr15:93444024-93555676	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
9	nsv917347	chr15:93444094-93586814	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12903587	CIB1	cis	cerebellum	SCAN
rs12903587	FAM174B	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93448200-93456600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:93448600-93457400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr15:93448600-93459200	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr15:93449000-93457600	Enhancers	Primary hematopoietic stem cells	blood
5	chr15:93449400-93457600	Genic enhancers	Primary B cells from peripheral blood	blood
6	chr15:93449600-93455600	Genic enhancers	Dnd41	blood
7	chr15:93449800-93460800	Enhancers	Stomach Mucosa	stomach
8	chr15:93450600-93459600	Genic enhancers	Fetal Thymus	thymus
9	chr15:93451000-93455600	Genic enhancers	Fetal Intestine Large	intestine
10	chr15:93451600-93456600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:93451600-93458000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr15:93451800-93455800	Genic enhancers	Thymus	Thymus
13	chr15:93451800-93456400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
14	chr15:93451800-93464000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr15:93452000-93456400	Genic enhancers	Primary B cells from cord blood	blood
16	chr15:93452000-93457200	Enhancers	Psoas Muscle	Psoas
17	chr15:93452000-93457600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr15:93452000-93457600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr15:93452000-93457800	Genic enhancers	Hela-S3	cervix
20	chr15:93452000-93458400	Enhancers	Right Atrium	heart
21	chr15:93452000-93461000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr15:93452200-93455600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr15:93452200-93457800	Enhancers	Brain Anterior Caudate	brain
24	chr15:93452400-93456600	Weak transcription	Fetal Brain Male	brain
25	chr15:93452600-93455600	Genic enhancers	Left Ventricle	heart
26	chr15:93452600-93455800	Genic enhancers	Fetal Muscle Leg	muscle
27	chr15:93452600-93456400	Weak transcription	Brain Germinal Matrix	brain
28	chr15:93452800-93455600	Genic enhancers	Rectal Mucosa Donor 29	rectum
29	chr15:93452800-93457000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr15:93452800-93457000	Genic enhancers	A549	lung
31	chr15:93453000-93455600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr15:93453000-93455600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr15:93453000-93456000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr15:93453000-93457000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr15:93453400-93455600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr15:93453800-93455600	Strong transcription	Fetal Muscle Trunk	muscle
37	chr15:93453800-93456000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr15:93453800-93456200	Strong transcription	Fetal Stomach	stomach
39	chr15:93453800-93458200	Enhancers	Small Intestine	intestine
40	chr15:93453800-93458600	Enhancers	Brain Angular Gyrus	brain
41	chr15:93453800-93459400	Genic enhancers	K562	blood
42	chr15:93454000-93456600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr15:93454000-93456800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr15:93454000-93457200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr15:93454000-93457600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr15:93454000-93460600	Weak transcription	Ovary	ovary
47	chr15:93454000-93464000	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr15:93454200-93455600	Genic enhancers	Rectal Smooth Muscle	rectum
49	chr15:93454200-93456200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr15:93454200-93456200	Enhancers	Right Ventricle	heart

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