Variant report

Variant	rs930920
Chromosome Location	chr15:51749726-51749727
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:51745144..51748040-chr15:51748185..51750918,2	K562	blood:

Variant related genes	Relation type
ENSG00000104093	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1031664	0.88[CEU][hapmap];0.80[AMR][1000 genomes]
rs10467923	0.89[CEU][hapmap];0.83[GIH][hapmap];0.87[MEX][hapmap]
rs10467924	0.82[AMR][1000 genomes]
rs10519313	0.81[CEU][hapmap];0.85[GIH][hapmap];0.84[MEX][hapmap];0.89[YRI][hapmap]
rs10775144	0.88[CEU][hapmap]
rs1080394	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10851500	0.82[AMR][1000 genomes]
rs10851502	0.83[CEU][hapmap];1.00[YRI][hapmap]
rs11070851	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11070853	0.81[AMR][1000 genomes]
rs11070854	0.84[AMR][1000 genomes]
rs11070857	0.89[CEU][hapmap];0.82[GIH][hapmap]
rs11070859	0.85[CEU][hapmap];0.92[YRI][hapmap]
rs11070862	0.84[CEU][hapmap];0.83[YRI][hapmap]
rs11630336	0.81[AFR][1000 genomes]
rs11630842	0.87[GIH][hapmap];0.84[MEX][hapmap]
rs11631408	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11632853	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs11633713	0.85[CEU][hapmap];0.89[YRI][hapmap]
rs11634110	0.82[AMR][1000 genomes]
rs11634180	0.88[CEU][hapmap];0.95[YRI][hapmap]
rs11635216	0.85[CEU][hapmap];0.85[GIH][hapmap]
rs11635592	0.84[CEU][hapmap]
rs11636170	0.85[CEU][hapmap];0.81[AMR][1000 genomes]
rs12101920	0.81[AMR][1000 genomes]
rs12372948	0.84[CEU][hapmap];0.83[GIH][hapmap]
rs12438892	0.89[CEU][hapmap];0.96[YRI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12440990	0.84[CEU][hapmap];1.00[YRI][hapmap]
rs12441759	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12443362	0.81[AFR][1000 genomes]
rs12592179	0.85[AMR][1000 genomes]
rs12593979	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12913493	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs17524813	0.86[AMR][1000 genomes]
rs17603116	0.86[AMR][1000 genomes]
rs2124592	0.81[CEU][hapmap];0.92[YRI][hapmap]
rs2124875	0.88[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2124876	0.85[CEU][hapmap];0.88[YRI][hapmap]
rs2124878	0.88[CEU][hapmap];0.88[YRI][hapmap]
rs2124879	0.85[YRI][hapmap]
rs2278989	0.81[CEU][hapmap];0.85[GIH][hapmap];0.84[MEX][hapmap];0.89[YRI][hapmap]
rs2278990	0.81[CEU][hapmap];0.85[GIH][hapmap];0.84[MEX][hapmap];0.89[YRI][hapmap]
rs2305708	0.84[CEU][hapmap];0.89[YRI][hapmap]
rs2414105	0.85[GIH][hapmap]
rs2414106	0.85[CEU][hapmap];0.85[GIH][hapmap];0.84[MEX][hapmap];0.89[YRI][hapmap]
rs2414109	0.85[CEU][hapmap];0.85[GIH][hapmap];0.84[MEX][hapmap];0.89[YRI][hapmap]
rs2414111	0.85[CEU][hapmap];0.86[GIH][hapmap];0.89[YRI][hapmap]
rs28415556	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28431083	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs28680710	0.87[AMR][1000 genomes]
rs28854610	0.87[AMR][1000 genomes]
rs28878886	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3736485	0.85[CEU][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4143722	0.81[AFR][1000 genomes]
rs4462537	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4774589	0.81[AMR][1000 genomes]
rs4774591	0.89[CEU][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4774592	0.82[AMR][1000 genomes]
rs4774593	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs4774597	0.96[YRI][hapmap]
rs4775943	0.88[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4775944	0.85[CEU][hapmap];0.82[AMR][1000 genomes]
rs4775946	0.85[CEU][hapmap];0.82[AMR][1000 genomes]
rs4775953	0.85[CEU][hapmap];0.85[GIH][hapmap];0.84[MEX][hapmap];0.89[YRI][hapmap]
rs4775955	0.85[CEU][hapmap];0.80[GIH][hapmap];0.80[MEX][hapmap];0.89[YRI][hapmap]
rs4775960	0.85[CEU][hapmap];0.83[GIH][hapmap];0.84[MEX][hapmap];0.89[YRI][hapmap]
rs4775961	0.85[CEU][hapmap];0.83[GIH][hapmap];0.84[MEX][hapmap];0.82[YRI][hapmap]
rs55981933	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs62014659	0.86[AMR][1000 genomes]
rs6493498	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs6493499	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs6493500	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs6493501	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs6493503	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs6493505	0.85[CEU][hapmap];0.92[YRI][hapmap]
rs67524810	0.82[AMR][1000 genomes]
rs7162412	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7162563	0.87[AMR][1000 genomes]
rs7164265	0.83[AFR][1000 genomes]
rs7165887	0.87[GIH][hapmap];0.84[MEX][hapmap]
rs7167760	0.81[CEU][hapmap];0.84[GIH][hapmap];0.88[MEX][hapmap];0.84[YRI][hapmap]
rs7170217	0.88[CEU][hapmap];0.96[YRI][hapmap]
rs7170444	0.81[CEU][hapmap];0.95[YRI][hapmap]
rs7174435	0.84[CEU][hapmap];0.89[YRI][hapmap]
rs7174495	0.92[CEU][hapmap];1.00[YRI][hapmap]
rs7177471	0.84[CEU][hapmap]
rs7177720	0.84[CEU][hapmap];0.83[GIH][hapmap];0.84[MEX][hapmap];0.89[YRI][hapmap]
rs7181470	0.83[AMR][1000 genomes]
rs7183479	0.80[CEU][hapmap];0.84[YRI][hapmap]
rs750162	0.85[CEU][hapmap];0.85[YRI][hapmap]
rs8023455	0.80[CEU][hapmap];0.88[YRI][hapmap]
rs8024506	0.90[AMR][1000 genomes]
rs8037167	0.81[CEU][hapmap];0.85[GIH][hapmap];0.84[MEX][hapmap];0.89[YRI][hapmap]
rs8038101	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8038341	0.81[AFR][1000 genomes]
rs8039073	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8040080	0.85[CEU][hapmap];0.88[YRI][hapmap]
rs8042221	0.84[CEU][hapmap];0.85[GIH][hapmap];0.82[AMR][1000 genomes]
rs8042289	0.88[CEU][hapmap];0.86[YRI][hapmap]
rs8042840	0.85[CEU][hapmap];0.85[GIH][hapmap];0.84[MEX][hapmap];0.89[YRI][hapmap]
rs9944241	0.81[CEU][hapmap];0.85[GIH][hapmap];0.84[MEX][hapmap];0.89[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569400	chr15:50874964-51767265	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	esv34532	chr15:51276128-51752856	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	esv2758382	chr15:51282257-51830339	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	esv2760031	chr15:51282257-51830339	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv471243	chr15:51345485-52018096	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	esv2757600	chr15:51352249-51783981	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv904217	chr15:51695653-51881980	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv904218	chr15:51743186-51873407	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs930920	SCG3	cis	cerebellum	SCAN
rs930920	DMXL2	Cis_1M	lymphoblastoid	RTeQTL
rs930920	DMXL2	cis	lymphoblastoid	seeQTL
rs930920	SQRDL	cis	cerebellum	SCAN
rs930920	ARPP19	cis	parietal	SCAN
rs930920	BCL2L10	cis	parietal	SCAN
rs930920	TMOD2	cis	parietal	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51736800-51751200	Weak transcription	HUVEC	blood vessel
2	chr15:51737000-51775600	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr15:51737000-51776400	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr15:51737400-51750200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr15:51737600-51762400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr15:51737800-51758400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr15:51737800-51762400	Weak transcription	Colonic Mucosa	Colon
8	chr15:51738000-51755400	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr15:51738200-51784600	Weak transcription	Stomach Mucosa	stomach
10	chr15:51738400-51777400	Weak transcription	Small Intestine	intestine
11	chr15:51738600-51751800	Strong transcription	Rectal Mucosa Donor 31	rectum
12	chr15:51738800-51752000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr15:51738800-51752200	Strong transcription	Fetal Intestine Large	intestine
14	chr15:51738800-51752600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr15:51739000-51750200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:51739000-51752000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr15:51739000-51752000	Strong transcription	Liver	Liver
18	chr15:51739000-51776000	Weak transcription	Gastric	stomach
19	chr15:51740200-51751800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr15:51740600-51751800	Weak transcription	Psoas Muscle	Psoas
21	chr15:51740800-51775200	Weak transcription	Pancreas	Pancrea
22	chr15:51741000-51753200	Weak transcription	HepG2	liver
23	chr15:51741200-51751000	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr15:51742400-51764800	Weak transcription	Primary B cells from cord blood	blood
25	chr15:51742400-51775800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr15:51742600-51749800	Weak transcription	NH-A	brain
27	chr15:51742600-51751000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr15:51742600-51751600	Strong transcription	A549	lung
29	chr15:51742600-51762000	Weak transcription	Spleen	Spleen
30	chr15:51742600-51762200	Weak transcription	Aorta	Aorta
31	chr15:51742600-51775400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr15:51742600-51775400	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr15:51742600-51776000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr15:51742600-51776600	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr15:51742600-51776800	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr15:51743000-51774200	Weak transcription	HMEC	breast
37	chr15:51743000-51775200	Weak transcription	HSMMtube	muscle
38	chr15:51743000-51780200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr15:51743600-51769600	Weak transcription	HSMM	muscle
40	chr15:51744400-51754000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr15:51745800-51751200	Strong transcription	Hela-S3	cervix
42	chr15:51745800-51752000	Strong transcription	Brain Anterior Caudate	brain
43	chr15:51745800-51752000	Strong transcription	Placenta	Placenta
44	chr15:51745800-51755200	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr15:51746000-51752000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr15:51746200-51751800	Strong transcription	Fetal Brain Female	brain
47	chr15:51746200-51752600	Strong transcription	Brain Inferior Temporal Lobe	brain
48	chr15:51746400-51749800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr15:51746400-51751800	Strong transcription	Duodenum Mucosa	Duodenum
50	chr15:51746400-51751800	Strong transcription	Fetal Lung	lung

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