Variant report

Variant	rs731831
Chromosome Location	chr3:52536514-52536515
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52504996..52506918-chr3:52535565..52538055,2	MCF-7	breast:
2	chr3:52529207..52530741-chr3:52535471..52537071,2	K562	blood:
3	chr3:52535446..52537192-chr3:52550633..52552577,2	K562	blood:
4	chr3:52488122..52489688-chr3:52535333..52537120,2	K562	blood:
5	chr3:52535112..52538485-chr3:52564476..52567424,4	K562	blood:
6	chr3:52532062..52534916-chr3:52535199..52537993,2	K562	blood:
7	chr3:52536407..52539525-chr3:52571038..52574825,3	K562	blood:
8	chr3:52535025..52537846-chr3:52565784..52568503,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000168273	Chromatin interaction
ENSG00000010322	Chromatin interaction
ENSG00000168268	Chromatin interaction
ENSG00000010327	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 25 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1010552	0.84[CHB][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1010553	0.81[CHB][hapmap];0.86[CHD][hapmap];0.84[ASN][1000 genomes]
rs1010554	0.91[CHB][hapmap];0.84[CHD][hapmap]
rs10510760	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap]
rs10865973	0.82[CHB][hapmap]
rs10865974	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs1108842	0.82[CHB][hapmap]
rs11130306	0.86[ASN][1000 genomes]
rs11130310	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs11130312	0.82[CHB][hapmap]
rs11130315	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs11130317	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs11177	0.82[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.80[MEX][hapmap]
rs1133415	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs11714419	0.82[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap]
rs11714565	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs11720159	0.82[CHB][hapmap]
rs11720243	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs12487445	0.81[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap]
rs12487591	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs12488461	0.82[CHB][hapmap];0.80[CHD][hapmap];0.91[GIH][hapmap]
rs12489732	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12489828	0.90[CHB][hapmap]
rs12496634	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs13063160	0.88[CHD][hapmap]
rs13064064	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs13068293	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs13081028	0.87[CHB][hapmap];0.81[CHD][hapmap]
rs13083798	0.82[CHB][hapmap]
rs13085775	0.81[CHD][hapmap]
rs13085895	0.82[CHB][hapmap]
rs13094687	0.90[CEU][hapmap]
rs13303	0.86[CHB][hapmap];0.81[CHD][hapmap]
rs1546737	0.90[CEU][hapmap]
rs1561337	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs17052256	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs17052259	0.82[CHB][hapmap]
rs17264436	0.81[CHB][hapmap]
rs1866268	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs1961958	0.86[CHD][hapmap];0.86[GIH][hapmap];0.80[MEX][hapmap]
rs2015971	0.87[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs2028216	0.82[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.80[MEX][hapmap]
rs2083180	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs2118540	0.81[CEU][hapmap]
rs2164884	0.81[CHB][hapmap]
rs2164885	0.81[CHB][hapmap];0.85[CHD][hapmap]
rs2251219	0.82[CHB][hapmap];0.84[CHD][hapmap]
rs2272088	0.90[CEU][hapmap]
rs2276824	0.82[CHB][hapmap]
rs2289247	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs2289249	0.82[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap]
rs2289250	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs2336146	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs2336149	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs2577831	0.82[CHB][hapmap]
rs2590838	0.82[CHB][hapmap]
rs2878628	0.82[CHB][hapmap];0.86[CHD][hapmap]
rs33967311	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs34736619	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3733039	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs3733041	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs3733045	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs3755806	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs3774365	0.82[CHB][hapmap]
rs3774366	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs3796353	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs3844291	0.90[CEU][hapmap]
rs3852064	0.90[CEU][hapmap]
rs3852066	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs4282054	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs4475032	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs4687548	0.82[CHB][hapmap]
rs4687625	0.85[CHB][hapmap]
rs4687626	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs4687629	0.82[CHB][hapmap]
rs4687638	0.82[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.80[MEX][hapmap]
rs6445528	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs6762813	0.82[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.80[MEX][hapmap]
rs6778735	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs6778844	0.82[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.80[MEX][hapmap]
rs6786043	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs6786919	0.81[CHB][hapmap];0.88[CHD][hapmap]
rs6798246	0.82[CHB][hapmap]
rs6804145	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs6805156	0.82[CHB][hapmap]
rs6976	0.82[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];0.80[MEX][hapmap]
rs7611731	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs7614981	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs7622694	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs7638808	0.86[CHB][hapmap];0.90[CHD][hapmap]
rs7652191	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs9853056	0.86[CHB][hapmap];0.83[CHD][hapmap]
rs9879090	0.85[CHB][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	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv834697	chr3:52400578-52579417	Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv876792	chr3:52430526-52575831	Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv876793	chr3:52450043-52584787	Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	esv1818902	chr3:52481406-52572056	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
7	nsv590305	chr3:52535586-52569480	Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv590306	chr3:52536308-52557440	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:25)

SNP	Gene	Cis/trans	Tissue	Source
rs731831	FLJ12442	cis	multi-tissue	Pritchard
rs731831	GNL3	cis	cerebellum	SCAN
rs731831	MUSTN1	cis	Artery Aorta	GTEx
rs731831	ITIH4	cis	parietal	SCAN
rs731831	ITIH3	cis	parietal	SCAN
rs731831	NT5DC2	cis	parietal	SCAN
rs731831	NEK4	cis	parietal	SCAN
rs731831	PBRM1	cis	Artery Tibial	GTEx
rs731831	GNL3	cis	parietal	SCAN
rs731831	ITIH4	cis	cerebellum	SCAN
rs731831	RBM6	cis	cerebellum	SCAN
rs731831	ITIH4-AS1	cis	Artery Aorta	GTEx
rs731831	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs731831	TMEM110	cis	cerebellum	SCAN
rs731831	SPCS1	cis	parietal	SCAN
rs731831	NEK4	cis	cerebellum	SCAN
rs731831	NT5DC2	cis	Skin Sun Exposed Lower leg	GTEx
rs731831	NT5DC2	cis	lymphoblastoid	seeQTL
rs731831	GLT8D1	cis	lymphoblastoid	seeQTL
rs731831	ITIH4	cis	lymphoblastoid	seeQTL
rs731831	CACNA2D3	cis	parietal	SCAN
rs731831	TMEM110	cis	parietal	SCAN
rs731831	RBM6	cis	parietal	SCAN
rs731831	GLT8D1	Cis_1M	lymphoblastoid	RTeQTL
rs731831	PBRM1	cis	Thyroid	GTEx

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52513400-52541400	Weak transcription	A549	lung
2	chr3:52527000-52538000	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr3:52527000-52540200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:52529200-52537400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:52530000-52537600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr3:52530000-52538800	Weak transcription	Gastric	stomach
7	chr3:52530200-52537600	Weak transcription	Pancreas	Pancrea
8	chr3:52530200-52551800	Weak transcription	Esophagus	oesophagus
9	chr3:52530400-52552400	Weak transcription	Brain Substantia Nigra	brain
10	chr3:52530600-52558000	Weak transcription	Colon Smooth Muscle	Colon
11	chr3:52530800-52537600	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr3:52530800-52548200	Weak transcription	Right Ventricle	heart
13	chr3:52530800-52551600	Weak transcription	Fetal Intestine Small	intestine
14	chr3:52531000-52547600	Weak transcription	Duodenum Mucosa	Duodenum
15	chr3:52532400-52536800	Genic enhancers	Spleen	Spleen
16	chr3:52533400-52540800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:52533400-52549200	Weak transcription	Fetal Muscle Leg	muscle
18	chr3:52533400-52549200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr3:52533400-52558200	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr3:52533400-52559800	Weak transcription	Liver	Liver
21	chr3:52533600-52537800	Weak transcription	Colonic Mucosa	Colon
22	chr3:52533600-52566000	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr3:52534600-52536600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr3:52535200-52538600	Weak transcription	Placenta	Placenta
25	chr3:52535400-52536800	Weak transcription	Adipose Nuclei	Adipose
26	chr3:52535400-52538800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:52535400-52539800	Strong transcription	HUVEC	blood vessel
28	chr3:52535400-52562200	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr3:52535600-52541600	Strong transcription	Lung	lung
30	chr3:52535600-52562600	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr3:52536000-52537400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr3:52536200-52536800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr3:52536200-52536800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr3:52536400-52537000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr3:52536400-52538600	Enhancers	Fetal Muscle Trunk	muscle

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