Variant report

Variant	rs715338
Chromosome Location	chr15:57215867-57215868
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57213938..57216093-chr15:57393779..57396458,2	MCF-7	breast:
2	chr15:57215422..57217856-chr15:57225443..57228595,3	K562	blood:

Extended variants
information (count: 102 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10518894	0.94[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap]
rs10518895	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs11630195	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.86[ASN][1000 genomes]
rs11631228	0.89[ASN][1000 genomes]
rs11631541	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap]
rs11631732	0.95[AFR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11632592	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11852340	0.94[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap]
rs11855648	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap]
rs11858471	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12437713	0.95[YRI][hapmap]
rs12898327	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12899187	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12899915	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs12900589	0.85[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.94[YRI][hapmap]
rs12900874	0.86[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap]
rs12900986	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.89[ASN][1000 genomes]
rs12901780	0.88[ASN][1000 genomes]
rs12904070	0.82[ASN][1000 genomes]
rs12904784	0.95[AFR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12905900	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12906873	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.86[ASN][1000 genomes]
rs12906936	0.86[ASN][1000 genomes]
rs12908670	0.89[ASN][1000 genomes]
rs12914625	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs12916237	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12916958	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12917247	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs13313455	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs1430823	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1628067	0.85[CHB][hapmap];0.86[JPT][hapmap];0.84[TSI][hapmap]
rs16953316	1.00[YRI][hapmap]
rs16977155	1.00[YRI][hapmap]
rs16977181	1.00[YRI][hapmap]
rs16977199	1.00[YRI][hapmap]
rs16977201	1.00[YRI][hapmap]
rs16977217	1.00[YRI][hapmap]
rs16977218	1.00[YRI][hapmap]
rs16977235	0.95[YRI][hapmap]
rs16977242	0.95[YRI][hapmap]
rs16977245	0.89[YRI][hapmap]
rs17239040	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17415738	0.95[YRI][hapmap]
rs17819700	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1820995	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs2053472	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2111891	0.93[ASN][1000 genomes]
rs2116065	0.89[ASN][1000 genomes]
rs2116066	0.89[ASN][1000 genomes]
rs213149	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs213164	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2165461	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2414490	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2464429	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs2464430	0.84[CHB][hapmap];0.91[JPT][hapmap]
rs2470079	0.84[CHB][hapmap];0.91[JPT][hapmap]
rs2470082	0.80[CHB][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.91[TSI][hapmap]
rs2583108	0.92[ASN][1000 genomes]
rs2585082	0.89[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.89[ASN][1000 genomes]
rs2585087	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs2585088	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs2585102	0.89[CHB][hapmap];0.91[JPT][hapmap]
rs2585112	0.84[CHB][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap]
rs2615231	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs2703576	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs2703580	0.82[GIH][hapmap];0.91[JPT][hapmap];0.89[TSI][hapmap]
rs2733170	0.80[CHB][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap];0.91[TSI][hapmap]
rs2733171	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs2733174	0.89[CHB][hapmap];0.91[JPT][hapmap]
rs2733188	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs2733332	0.89[CHB][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.87[TSI][hapmap]
rs2920267	0.84[CHB][hapmap];0.91[JPT][hapmap]
rs2951899	0.81[JPT][hapmap];0.89[TSI][hapmap]
rs2951901	0.80[CHB][hapmap];0.91[JPT][hapmap]
rs2951903	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs2951904	0.84[CHB][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap]
rs2962990	0.85[CHB][hapmap];0.91[JPT][hapmap];0.89[TSI][hapmap]
rs2962991	0.85[CHB][hapmap];0.90[JPT][hapmap]
rs2962992	0.80[GIH][hapmap];0.85[JPT][hapmap];0.91[TSI][hapmap]
rs2962993	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs34262415	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.89[ASN][1000 genomes]
rs35646942	0.87[ASN][1000 genomes]
rs3803454	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3803455	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41472450	1.00[YRI][hapmap]
rs4399497	0.92[AFR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4774898	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4774899	0.96[ASN][1000 genomes]
rs4774902	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.92[ASN][1000 genomes]
rs4774910	0.85[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs62025331	0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6493901	0.84[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs7170133	0.82[ASN][1000 genomes]
rs7183392	0.95[YRI][hapmap]
rs7496293	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[ASN][1000 genomes]
rs967514	0.85[CHB][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.89[TSI][hapmap]

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	esv3422474	chr15:56867190-57244330	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv833020	chr15:57055947-57216068	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv457162	chr15:57083006-57225766	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv569577	chr15:57083006-57225766	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv1042486	chr15:57094598-57505992	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv542393	chr15:57115116-57341363	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription 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	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs715338	GCOM1	cis	cerebellum	SCAN
rs715338	RAB27A	cis	cerebellum	SCAN
rs715338	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57209400-57217200	Active TSS	Thymus	Thymus
2	chr15:57211400-57216000	Transcr. at gene 5' and 3'	Dnd41	blood
3	chr15:57212400-57218200	Weak transcription	Small Intestine	intestine
4	chr15:57212400-57219000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr15:57212400-57222000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr15:57212400-57224800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr15:57212400-57224800	Weak transcription	Spleen	Spleen
8	chr15:57212400-57230400	Weak transcription	Lung	lung
9	chr15:57212400-57233400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr15:57212400-57256000	Weak transcription	Pancreas	Pancrea
11	chr15:57212600-57218200	Weak transcription	Aorta	Aorta
12	chr15:57212600-57224000	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr15:57212600-57241000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr15:57212800-57218200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr15:57212800-57218600	Weak transcription	Fetal Stomach	stomach
16	chr15:57212800-57219200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr15:57212800-57220200	Weak transcription	Primary B cells from peripheral blood	blood
18	chr15:57212800-57220600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:57212800-57222200	Weak transcription	Left Ventricle	heart
20	chr15:57212800-57222200	Weak transcription	Psoas Muscle	Psoas
21	chr15:57212800-57222200	Weak transcription	Right Ventricle	heart
22	chr15:57212800-57222400	Weak transcription	Ovary	ovary
23	chr15:57212800-57224000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr15:57212800-57227200	Weak transcription	Fetal Muscle Trunk	muscle
25	chr15:57213000-57216000	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr15:57213000-57216800	Weak transcription	Fetal Muscle Leg	muscle
27	chr15:57213000-57218600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr15:57213000-57219400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr15:57213000-57220800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr15:57213000-57222200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr15:57213000-57222400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr15:57213000-57227400	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr15:57213200-57216400	Weak transcription	NHDF-Ad	bronchial
34	chr15:57213200-57216600	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr15:57213200-57218600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr15:57213200-57218600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
37	chr15:57213200-57221000	Weak transcription	Adipose Nuclei	Adipose
38	chr15:57213200-57221200	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr15:57213200-57223400	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr15:57213200-57256000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr15:57213400-57216000	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr15:57213400-57216200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr15:57213400-57217000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr15:57213400-57217600	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr15:57213400-57218200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr15:57213400-57219000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr15:57213400-57219000	Weak transcription	HSMMtube	muscle
48	chr15:57213400-57220200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr15:57213400-57220200	Weak transcription	NHEK	skin
50	chr15:57213400-57223200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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