Variant report

Variant	rs2304582
Chromosome Location	chr15:41030865-41030866
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:41030576-41030998	GM12892	blood:	n/a	n/a
2	POLR2A	chr15:41030626-41030868	GM12878	blood:	n/a	n/a
3	POLR2A	chr15:41030676-41030872	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr15:41030713-41030933	MCF-7	breast:	n/a	n/a
5	POLR2A	chr15:41030560-41030994	K562	blood:	n/a	n/a
6	POLR2A	chr15:41030614-41030950	K562	blood:	n/a	n/a
7	POLR2A	chr15:41030565-41030906	GM12891	blood:	n/a	n/a
8	POLR2A	chr15:41030642-41030985	PFSK-1	brain:	n/a	n/a
9	POLR2A	chr15:41030546-41030933	K562	blood:	n/a	n/a
10	POLR2A	chr15:41030620-41033888	K562	blood:	n/a	n/a
11	POLR2A	chr15:41030605-41030925	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr15:41030717-41030957	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41029851..41031693-chr15:41035155..41036764,2	K562	blood:

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

Extended variants
information (count: 58 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10775121	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11070291	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11070293	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11631563	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11633269	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11852786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11855560	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11858337	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11858338	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12372947	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12439683	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12441514	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12442845	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12593359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12908284	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2263551	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2412546	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2412547	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2412548	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2412549	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2577564	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2619679	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2619680	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2619681	0.81[YRI][hapmap]
rs2619683	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2917955	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2928140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3092982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3092983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3101861	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34400306	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs36106105	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs45495293	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4923884	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4924493	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4924495	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4924500	0.80[YRI][hapmap]
rs4924501	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4924503	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56042757	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6492961	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7164339	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7167854	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7169010	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7172195	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7173646	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7174551	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7175401	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs752012	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8025883	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8033829	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8036817	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	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	nsv527234	chr15:40987725-41031686	Transcr. at gene 5' and 3' Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2304582	C15orf57	cis	Artery Tibial	GTEx
rs2304582	RAD51	cis	multi-tissue	Pritchard
rs2304582	C15orf57	cis	lung	GTEx
rs2304582	RP11-111A22.1	cis	Artery Tibial	GTEx
rs2304582	RAD51	Cis_1M	lymphoblastoid	RTeQTL
rs2304582	C15orf57	cis	Nerve Tibial	GTEx
rs2304582	RP11-111A22.1	cis	lung	GTEx
rs2304582	CCDC32	cis	multi-tissue	Pritchard
rs2304582	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs2304582	C15orf57	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40988400-41031000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:40998800-41038000	Weak transcription	Stomach Mucosa	stomach
3	chr15:41008200-41046600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr15:41019200-41035600	Weak transcription	Fetal Heart	heart
5	chr15:41019400-41036000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr15:41019400-41046200	Strong transcription	Fetal Stomach	stomach
7	chr15:41019600-41036200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:41019600-41036200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr15:41020000-41036000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr15:41020000-41043600	Strong transcription	Dnd41	blood
11	chr15:41020400-41035600	Strong transcription	K562	blood
12	chr15:41020400-41035800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr15:41020400-41036000	Strong transcription	Fetal Thymus	thymus
14	chr15:41020400-41037600	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr15:41020600-41033600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr15:41020600-41036000	Strong transcription	Placenta	Placenta
17	chr15:41020600-41036800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr15:41020600-41037800	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr15:41020600-41038200	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr15:41020800-41032600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr15:41020800-41035600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr15:41020800-41035600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr15:41020800-41045400	Strong transcription	Fetal Muscle Trunk	muscle
24	chr15:41021400-41033400	Strong transcription	Fetal Brain Female	brain
25	chr15:41021600-41032800	Strong transcription	Osteobl	bone
26	chr15:41021600-41033600	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr15:41021600-41034800	Strong transcription	Fetal Intestine Large	intestine
28	chr15:41021600-41035800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr15:41021600-41035800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr15:41021600-41036000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr15:41021800-41034200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr15:41021800-41044600	Strong transcription	Brain Germinal Matrix	brain
33	chr15:41023200-41035600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr15:41023200-41045200	Strong transcription	Thymus	Thymus
35	chr15:41023400-41034600	Strong transcription	Fetal Intestine Small	intestine
36	chr15:41023600-41036200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr15:41023600-41036800	Strong transcription	Fetal Muscle Leg	muscle
38	chr15:41023800-41031200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr15:41023800-41032600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr15:41023800-41038400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr15:41023800-41045200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr15:41024200-41031600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr15:41024600-41035400	Strong transcription	Skeletal Muscle Male	skeletal muscle
44	chr15:41024800-41033600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr15:41024800-41034000	Strong transcription	Primary B cells from peripheral blood	blood
46	chr15:41025400-41032600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr15:41025400-41035600	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr15:41025400-41036000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr15:41025600-41032400	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr15:41025600-41035400	Strong transcription	Liver	Liver

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