Variant report

Variant	rs2304579
Chromosome Location	chr15:40991153-40991154
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:40990437..40992433-chr15:41186523..41189273,2	K562	blood:
2	chr15:40990811..40992810-chr15:41055825..41057654,2	MCF-7	breast:
3	chr15:40986558..40989601-chr15:40990368..40993764,9	K562	blood:

Variant related genes	Relation type
ENSG00000051180	Chromatin interaction
ENSG00000245849	Chromatin interaction
ENSG00000137880	Chromatin interaction
ENSG00000104142	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10518696	0.82[ASW][hapmap];1.00[CEU][hapmap];0.86[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.84[TSI][hapmap];0.92[YRI][hapmap];0.82[EUR][1000 genomes]
rs11070276	1.00[CEU][hapmap]
rs11632319	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs12442697	1.00[CEU][hapmap];1.00[MEX][hapmap]
rs12916218	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs1453182	1.00[CEU][hapmap]
rs1530942	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs1530943	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs16970854	1.00[CEU][hapmap];0.89[JPT][hapmap];0.92[YRI][hapmap];0.82[EUR][1000 genomes]
rs1801320	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1869303	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap]
rs2014367	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs2034653	0.88[JPT][hapmap]
rs2278887	0.82[GIH][hapmap];0.89[JPT][hapmap]
rs2278889	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs2290379	1.00[CEU][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap]
rs2412530	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs2924389	1.00[CEU][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap]
rs2959535	1.00[CEU][hapmap];0.88[JPT][hapmap]
rs3803354	1.00[CEU][hapmap];0.81[CHD][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap]
rs4144242	0.88[CHB][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4467046	0.89[JPT][hapmap]
rs45455000	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45503494	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45504895	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs45507396	0.98[EUR][1000 genomes]
rs45559631	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs45579836	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45585734	0.83[AFR][1000 genomes];0.98[EUR][1000 genomes]
rs4561439	1.00[CEU][hapmap]
rs4923877	1.00[CEU][hapmap];0.81[CHD][hapmap];0.89[JPT][hapmap]
rs4923878	1.00[CEU][hapmap];0.86[CHD][hapmap];0.89[MEX][hapmap]
rs4923879	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs4924482	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs4924483	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs5030786	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57140606	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs57736474	0.81[EUR][1000 genomes]
rs57936990	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58458955	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59654927	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60408076	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61381741	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6492955	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs7164166	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs7167922	1.00[CEU][hapmap]
rs73396510	0.81[EUR][1000 genomes]
rs73396515	0.81[EUR][1000 genomes]
rs8024579	1.00[CEU][hapmap];0.81[CHD][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap]
rs8024802	1.00[CEU][hapmap];0.81[CHD][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap]
rs8029208	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs8032453	1.00[CEU][hapmap]
rs8034726	1.00[CEU][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs8040187	1.00[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap]
rs8041816	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs8041991	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs896797	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs921624	1.00[CEU][hapmap];0.89[JPT][hapmap]
rs976402	1.00[CEU][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832984	chr15:40794391-40998535	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	esv2758378	chr15:40832545-40995111	Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv2760026	chr15:40832545-40995111	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	nsv529030	chr15:40956471-41012695	Active TSS Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv904100	chr15:40959624-40994706	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
9	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
10	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2304579	MRPL42P5	cis	multi-tissue	Pritchard

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40987800-40993600	Weak transcription	Lung	lung
2	chr15:40988000-40991600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr15:40988000-40999400	Weak transcription	Right Atrium	heart
4	chr15:40988000-41030000	Weak transcription	Pancreas	Pancrea
5	chr15:40988200-40991600	Weak transcription	Thymus	Thymus
6	chr15:40988200-40991800	Weak transcription	Esophagus	oesophagus
7	chr15:40988200-41001200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:40988200-41028600	Weak transcription	Spleen	Spleen
9	chr15:40988400-40998000	Weak transcription	Fetal Intestine Large	intestine
10	chr15:40988400-41020600	Weak transcription	Placenta	Placenta
11	chr15:40988400-41020800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr15:40988400-41021600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr15:40988400-41021800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr15:40988400-41027200	Weak transcription	Primary B cells from cord blood	blood
15	chr15:40988400-41031000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr15:40988600-40992000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr15:40988600-40992400	Weak transcription	Adipose Nuclei	Adipose
18	chr15:40988600-40994800	Weak transcription	Fetal Intestine Small	intestine
19	chr15:40988600-40998400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr15:40988600-41000800	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr15:40988600-41001200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr15:40988600-41007800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr15:40988600-41018400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr15:40988600-41021400	Weak transcription	Duodenum Mucosa	Duodenum
25	chr15:40988600-41021400	Weak transcription	Fetal Brain Female	brain
26	chr15:40988800-40991200	Weak transcription	NH-A	brain
27	chr15:40988800-40991600	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr15:40988800-40991600	Weak transcription	Fetal Muscle Trunk	muscle
29	chr15:40988800-40993200	Weak transcription	HSMM	muscle
30	chr15:40988800-40993400	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr15:40988800-40993600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr15:40988800-40998600	Weak transcription	Gastric	stomach
33	chr15:40988800-40998600	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr15:40988800-41000800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr15:40988800-41000800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr15:40988800-41000800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr15:40988800-41001200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr15:40988800-41002800	Weak transcription	Brain Germinal Matrix	brain
39	chr15:40988800-41020600	Weak transcription	Primary T cells from cord blood	blood
40	chr15:40988800-41021600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr15:40988800-41021800	Weak transcription	Fetal Kidney	kidney
42	chr15:40989000-40991400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr15:40989000-40991800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr15:40989000-40992400	Weak transcription	Osteobl	bone
45	chr15:40989000-41001000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr15:40989000-41001200	Weak transcription	Fetal Lung	lung
47	chr15:40989000-41012000	Weak transcription	NHLF	lung
48	chr15:40989000-41018000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr15:40989200-40991600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr15:40989200-40991600	Weak transcription	HepG2	liver

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