Variant report

Variant	rs2304583
Chromosome Location	chr15:41032138-41032139
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:40)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:40 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr15:41032115-41032269	HepG2	liver:	n/a	n/a
2	RAD21	chr15:41031960-41032523	HCT-116	colon:	n/a	n/a
3	GTF2F1	chr15:41032133-41032207	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr15:41031089-41032637	K562	blood:	n/a	n/a
5	CTCF	chr15:41032019-41032366	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr15:41032115-41032311	K562	blood:	n/a	n/a
7	RAD21	chr15:41032115-41032295	SK-N-SH_RA	brain:	n/a	n/a
8	CTCF	chr15:41032120-41032270	RPTEC	kidney:	n/a	n/a
9	CTCF	chr15:41032120-41032270	HPAF	blood vessel:	n/a	n/a
10	CTCF	chr15:41032060-41032210	HCFaa	heart:	n/a	n/a
11	POLR2A	chr15:41031407-41032331	GM12892	blood:	n/a	n/a
12	POLR2A	chr15:41032121-41032408	H1-hESC	embryonic stem cell:	n/a	n/a
13	CTCF	chr15:41032080-41032230	HPAF	blood vessel:	n/a	n/a
14	RAD21	chr15:41031995-41032296	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr15:41031321-41032585	Hela-S3	cervix:	n/a	n/a
16	RAD21	chr15:41032004-41032317	SK-N-SH_RA	brain:	n/a	n/a
17	POLR2A	chr15:41031314-41032581	PFSK-1	brain:	n/a	n/a
18	RAD21	chr15:41032061-41032369	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr15:41031824-41032433	GM12891	blood:	n/a	n/a
20	POLR2A	chr15:41031169-41032694	K562	blood:	n/a	n/a
21	POLR2A	chr15:41031905-41032641	MCF-7	breast:	n/a	n/a
22	CTCF	chr15:41032080-41032230	HRE	kidney:	n/a	n/a
23	CTCF	chr15:41032120-41032270	GM12875	blood:	n/a	n/a
24	POLR2A	chr15:41032035-41032704	GM12892	blood:	n/a	n/a
25	CTCF	chr15:41032040-41032310	A549	lung:	n/a	n/a
26	CTCF	chr15:41032080-41032230	AG04450	lung:	n/a	n/a
27	RAD21	chr15:41031952-41032436	H1-hESC	embryonic stem cell:	n/a	n/a
28	CTCF	chr15:41032080-41032230	HEEpiC	esophagus:	n/a	n/a
29	POLR2A	chr15:41031758-41032531	HL-60	blood:	n/a	n/a
30	POLR2A	chr15:41030620-41033888	K562	blood:	n/a	n/a
31	CTCF	chr15:41032120-41032270	HA-sp	spinal cord:	n/a	n/a
32	CTCF	chr15:41032120-41032270	AG09319	gingival:	n/a	n/a
33	CTCF	chr15:41032100-41032250	Hela-S3	cervix:	n/a	n/a
34	CTCF	chr15:41032100-41032250	HBMEC	blood vessel:	n/a	n/a
35	CTCF	chr15:41032087-41032401	MCF-7	breast:	n/a	n/a
36	CTCF	chr15:41032100-41032250	HMEC	breast:	n/a	n/a
37	CTCF	chr15:41032080-41032230	WERI-Rb-1	eye:	n/a	n/a
38	POLR2A	chr15:41031236-41032691	K562	blood:	n/a	n/a
39	POLR2A	chr15:41031501-41032539	K562	blood:	n/a	n/a
40	CTCF	chr15:41032080-41032230	HBMEC	blood vessel:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41031017..41033907-chr15:41037060..41039542,3	MCF-7	breast:
2	chr15:41030963..41032960-chr15:41046925..41048677,2	K562	blood:

No data

Variant related genes	Relation type
RMDN3	TF binding region
ENSG00000137824	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 30 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1051482	0.92[CEU][hapmap];0.88[CHB][hapmap];0.90[GIH][hapmap];0.93[MEX][hapmap];0.85[ASN][1000 genomes]
rs10851396	0.87[CEU][hapmap];0.88[CHB][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap]
rs11070279	0.87[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap]
rs11070290	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11852479	0.82[ASN][1000 genomes]
rs11855517	0.83[AMR][1000 genomes]
rs11855641	0.82[EUR][1000 genomes]
rs12148185	0.92[CEU][hapmap];0.88[CHB][hapmap];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12898552	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12906755	0.81[CEU][hapmap]
rs12907448	0.90[CEU][hapmap];0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs12908114	0.87[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap]
rs12908443	0.85[ASN][1000 genomes]
rs12910784	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12915563	0.83[CEU][hapmap];0.88[CHB][hapmap]
rs1453183	0.92[CEU][hapmap];0.88[CHB][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap]
rs17747399	0.82[ASN][1000 genomes]
rs2010300	0.92[CEU][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes]
rs2289219	0.92[CEU][hapmap];0.92[GIH][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs2412545	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2899000	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs34621344	0.86[EUR][1000 genomes]
rs34988257	0.89[EUR][1000 genomes]
rs36094699	0.83[AMR][1000 genomes]
rs3759796	0.86[EUR][1000 genomes]
rs4457966	0.91[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs45592734	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5030783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62018584	0.83[EUR][1000 genomes]
rs62019934	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs8025458	0.92[CEU][hapmap];1.00[MEX][hapmap]
rs8028910	0.87[CEU][hapmap]
rs8031427	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8038396	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9806410	0.91[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053173	chr15:40933163-41094127	Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv542363	chr15:40933163-41094127	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv904099	chr15:40949526-41041875	Genic enhancers Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
5	esv1819092	chr15:41017682-41255750	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases

mRNA abundance (count:30)

SNP	Gene	Cis/trans	Tissue	Source
rs2304583	C15orf57	cis	Artery Tibial	GTEx
rs2304583	C15orf57	cis	Cerebellum	GTEx
rs2304583	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL
rs2304583	RAD51	cis	multi-tissue	Pritchard
rs2304583	RP11-111A22.1	cis	Esophagus Muscularis	GTEx
rs2304583	C15orf57	cis	parietal	SCAN
rs2304583	C15orf57	cis	Nerve Tibial	GTEx
rs2304583	ZFYVE19	cis	parietal	SCAN
rs2304583	C15orf57	cis	Adipose Subcutaneous	GTEx
rs2304583	C15orf57	cis	Muscle Skeletal	GTEx
rs2304583	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs2304583	C15orf23	cis	parietal	SCAN
rs2304583	ZFYVE19	cis	multi-tissue	Pritchard
rs2304583	RAD51	Cis_1M	lymphoblastoid	RTeQTL
rs2304583	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx
rs2304583	C15orf57	cis	cerebellum	SCAN
rs2304583	MGC20481	cis	multi-tissue	Pritchard
rs2304583	C15orf57	cis	Artery Aorta	GTEx
rs2304583	C15orf57	cis	Lymphoblastoid	GTEx
rs2304583	C15orf57	cis	lung	GTEx
rs2304583	CCDC32	cis	multi-tissue	Pritchard
rs2304583	C15orf57	cis	lymphoblastoid	seeQTL
rs2304583	C15orf57	cis	Esophagus Mucosa	GTEx
rs2304583	C15orf57	cis	Stomach	GTEx
rs2304583	RP11-111A22.1	cis	Artery Tibial	GTEx
rs2304583	C15orf23	cis	cerebellum	SCAN
rs2304583	IVD	cis	cerebellum	SCAN
rs2304583	RP11-111A22.1	cis	lung	GTEx
rs2304583	C15orf57	cis	Esophagus Muscularis	GTEx
rs2304583	ZFYVE19	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40998800-41038000	Weak transcription	Stomach Mucosa	stomach
2	chr15:41008200-41046600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr15:41019200-41035600	Weak transcription	Fetal Heart	heart
4	chr15:41019400-41036000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr15:41019400-41046200	Strong transcription	Fetal Stomach	stomach
6	chr15:41019600-41036200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:41019600-41036200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr15:41020000-41036000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr15:41020000-41043600	Strong transcription	Dnd41	blood
10	chr15:41020400-41035600	Strong transcription	K562	blood
11	chr15:41020400-41035800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr15:41020400-41036000	Strong transcription	Fetal Thymus	thymus
13	chr15:41020400-41037600	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr15:41020600-41033600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr15:41020600-41036000	Strong transcription	Placenta	Placenta
16	chr15:41020600-41036800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr15:41020600-41037800	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr15:41020600-41038200	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr15:41020800-41032600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr15:41020800-41035600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr15:41020800-41035600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr15:41020800-41045400	Strong transcription	Fetal Muscle Trunk	muscle
23	chr15:41021400-41033400	Strong transcription	Fetal Brain Female	brain
24	chr15:41021600-41032800	Strong transcription	Osteobl	bone
25	chr15:41021600-41033600	Strong transcription	Cortex derived primary cultured neurospheres	brain
26	chr15:41021600-41034800	Strong transcription	Fetal Intestine Large	intestine
27	chr15:41021600-41035800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr15:41021600-41035800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr15:41021600-41036000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr15:41021800-41034200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr15:41021800-41044600	Strong transcription	Brain Germinal Matrix	brain
32	chr15:41023200-41035600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr15:41023200-41045200	Strong transcription	Thymus	Thymus
34	chr15:41023400-41034600	Strong transcription	Fetal Intestine Small	intestine
35	chr15:41023600-41036200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr15:41023600-41036800	Strong transcription	Fetal Muscle Leg	muscle
37	chr15:41023800-41032600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr15:41023800-41038400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr15:41023800-41045200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr15:41024600-41035400	Strong transcription	Skeletal Muscle Male	skeletal muscle
41	chr15:41024800-41033600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr15:41024800-41034000	Strong transcription	Primary B cells from peripheral blood	blood
43	chr15:41025400-41032600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr15:41025400-41035600	Strong transcription	Primary T helper cells PMA-I stimulated	--
45	chr15:41025400-41036000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr15:41025600-41032400	Strong transcription	Skeletal Muscle Female	skeletal muscle
47	chr15:41025600-41035400	Strong transcription	Liver	Liver
48	chr15:41025600-41035600	Strong transcription	Duodenum Mucosa	Duodenum
49	chr15:41025600-41045000	Strong transcription	Primary T cells from cord blood	blood
50	chr15:41025600-41045400	Strong transcription	Stomach Smooth Muscle	stomach

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