Variant report

Variant	rs11852670
Chromosome Location	chr15:40908904-40908905
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	chr15:40908832..40911175-chr15:40913134..40914934,3	K562	blood:
2	chr15:40907487..40910390-chr15:40913134..40917272,4	K562	blood:

Variant related genes	Relation type
ENSG00000137812	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 25 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1037445	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10400890	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10400901	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10444817	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11070277	0.82[EUR][1000 genomes]
rs11070282	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11070285	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070286	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632061	0.91[EUR][1000 genomes]
rs11632370	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11638742	0.82[EUR][1000 genomes]
rs11852694	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11852828	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11854986	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11855334	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11855923	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11856802	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858113	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11858938	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12591207	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12594548	0.82[EUR][1000 genomes]
rs12595610	0.82[EUR][1000 genomes]
rs12902568	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12904801	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12905162	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12912635	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12913697	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12914743	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16970851	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1811513	0.83[EUR][1000 genomes]
rs1813898	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1967368	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2412531	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2412532	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2412534	0.84[EUR][1000 genomes]
rs2412544	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2898996	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2924387	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2924388	0.82[EUR][1000 genomes]
rs2959536	0.81[EUR][1000 genomes]
rs3092979	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34845954	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35047458	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3751652	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3751653	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4080706	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4410047	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4923875	0.82[EUR][1000 genomes]
rs4923876	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4924478	0.82[EUR][1000 genomes]
rs4924479	0.82[EUR][1000 genomes]
rs4924480	0.82[EUR][1000 genomes]
rs4924481	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62019916	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62019918	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6492951	0.82[EUR][1000 genomes]
rs6582	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71471881	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7169621	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7181074	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7182530	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7183790	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7494968	0.80[EUR][1000 genomes]
rs8026605	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8029384	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8034043	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8034048	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8036737	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8038407	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8041534	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs896795	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs976401	0.84[EUR][1000 genomes]

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	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	esv1843830	chr15:40902453-40915045	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv1841263	chr15:40902453-40966765	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:25)

SNP	Gene	Cis/trans	Tissue	Source
rs11852670	C15orf57	cis	Muscle Skeletal	GTEx
rs11852670	RP11-111A22.1	cis	Muscle Skeletal	GTEx
rs11852670	RP11-111A22.1	cis	Stomach	GTEx
rs11852670	C15orf57	cis	Artery Aorta	GTEx
rs11852670	RP11-111A22.1	cis	Esophagus Muscularis	GTEx
rs11852670	C15orf57	cis	Esophagus Muscularis	GTEx
rs11852670	CCDC32	cis	multi-tissue	Pritchard
rs11852670	C15orf57	cis	Adipose Subcutaneous	GTEx
rs11852670	C15orf57	cis	Heart Left Ventricle	GTEx
rs11852670	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs11852670	C15orf57	cis	lung	GTEx
rs11852670	C15orf57	cis	Nerve Tibial	GTEx
rs11852670	RP11-111A22.1	cis	Nerve Tibial	GTEx
rs11852670	RP11-111A22.1	cis	lung	GTEx
rs11852670	C15orf57	cis	Esophagus Mucosa	GTEx
rs11852670	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL
rs11852670	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx
rs11852670	C15orf57	cis	Skin Sun Exposed Lower leg	GTEx
rs11852670	ZFYVE19	cis	multi-tissue	Pritchard
rs11852670	RP11-111A22.1	cis	Artery Tibial	GTEx
rs11852670	C15orf57	cis	Artery Tibial	GTEx
rs11852670	RP11-111A22.1	cis	Heart Left Ventricle	GTEx
rs11852670	C15orf57	cis	Thyroid	GTEx
rs11852670	RP11-111A22.1	cis	Artery Aorta	GTEx
rs11852670	C15orf57	cis	Stomach	GTEx

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40887600-40941800	Weak transcription	Fetal Intestine Large	intestine
2	chr15:40887800-40933200	Weak transcription	Duodenum Mucosa	Duodenum
3	chr15:40887800-40942200	Weak transcription	Primary B cells from cord blood	blood
4	chr15:40887800-40948200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr15:40887800-40961600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr15:40888000-40956000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr15:40888200-40912800	Weak transcription	HMEC	breast
8	chr15:40888400-40913200	Weak transcription	NHDF-Ad	bronchial
9	chr15:40888400-40913600	Weak transcription	NHLF	lung
10	chr15:40888400-40923200	Weak transcription	Osteobl	bone
11	chr15:40888400-40925800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr15:40888400-40944200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr15:40890800-40925200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr15:40893600-40922600	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr15:40896000-40910200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr15:40896800-40910400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr15:40897800-40957200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:40899400-40922600	Weak transcription	Fetal Intestine Small	intestine
19	chr15:40899600-40911600	Weak transcription	Fetal Muscle Trunk	muscle
20	chr15:40899600-40911800	Weak transcription	Fetal Muscle Leg	muscle
21	chr15:40899600-40913200	Weak transcription	Primary hematopoietic stem cells	blood
22	chr15:40900000-40943600	Weak transcription	NH-A	brain
23	chr15:40900200-40912800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr15:40900400-40913200	Weak transcription	NHEK	skin
25	chr15:40900600-40912800	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr15:40902000-40911200	Weak transcription	HepG2	liver
27	chr15:40902200-40920400	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr15:40902400-40911000	Weak transcription	HSMM	muscle
29	chr15:40902600-40911000	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr15:40902800-40911800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr15:40902800-40913000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr15:40903000-40909400	Weak transcription	K562	blood
33	chr15:40903000-40913000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr15:40903000-40922200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr15:40903000-40956000	Weak transcription	Fetal Heart	heart
36	chr15:40903200-40909800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr15:40903200-40911600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr15:40903200-40912800	Weak transcription	HUVEC	blood vessel
39	chr15:40903600-40911000	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr15:40903600-40912800	Weak transcription	GM12878-XiMat	blood
41	chr15:40903600-40913200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr15:40903600-40922600	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr15:40903600-40927800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr15:40903600-40956600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr15:40903800-40955800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr15:40903800-40956600	Weak transcription	Fetal Lung	lung
47	chr15:40904400-40911600	Weak transcription	Fetal Stomach	stomach
48	chr15:40904800-40927800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr15:40905200-40911200	Weak transcription	Thymus	Thymus
50	chr15:40905600-40912800	Weak transcription	HUES48 Cell Line	embryonic stem cell

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