Variant report

Variant	rs4264773
Chromosome Location	chr3:158463225-158463226
allele	G/T
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:158461573..158464400-chr3:158464739..158466515,2	K562	blood:
2	chr3:158461553..158464844-chr3:158481750..158486798,5	K562	blood:
3	chr3:158461736..158463794-chr3:158468012..158469829,2	K562	blood:
4	chr3:158460933..158463789-chr3:158476160..158478339,2	MCF-7	breast:
5	chr3:158458014..158460479-chr3:158462665..158465374,2	MCF-7	breast:
6	chr3:158460803..158463354-chr3:158491708..158495775,3	MCF-7	breast:
7	chr3:158439350..158441066-chr3:158462153..158464983,2	MCF-7	breast:
8	chr3:158463142..158465142-chr3:158474543..158477563,3	K562	blood:
9	chr3:158460535..158463569-chr3:158485290..158488167,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000118855	Chromatin interaction
ENSG00000240207	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs2115944	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55835802	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58152433	0.86[ASN][1000 genomes]
rs59217052	0.86[ASN][1000 genomes]
rs59313096	0.86[ASN][1000 genomes]
rs59918529	0.86[ASN][1000 genomes]
rs59957986	0.86[ASN][1000 genomes]
rs61080878	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61387735	0.86[ASN][1000 genomes]
rs61558956	0.86[ASN][1000 genomes]
rs61696028	0.86[ASN][1000 genomes]
rs6441222	0.86[ASN][1000 genomes]
rs67301795	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67305172	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67446837	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6775607	0.88[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6788069	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs73015644	0.86[ASN][1000 genomes]
rs73015651	0.86[ASN][1000 genomes]
rs73015652	0.86[ASN][1000 genomes]
rs73015654	0.86[ASN][1000 genomes]
rs73015655	0.86[ASN][1000 genomes]
rs73015657	0.86[ASN][1000 genomes]
rs73015665	0.86[ASN][1000 genomes]
rs73015669	0.86[ASN][1000 genomes]
rs73017536	0.86[ASN][1000 genomes]
rs73017539	0.86[ASN][1000 genomes]
rs73017540	0.86[ASN][1000 genomes]
rs73017541	0.86[ASN][1000 genomes]
rs73158329	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73158333	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73158334	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73158346	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7617304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7624161	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs7636023	0.86[ASN][1000 genomes]
rs7646881	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs7646987	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs9864589	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1014255	chr3:158358860-158768542	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv532665	chr3:158370013-158754245	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv948755	chr3:158388780-158672287	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv877692	chr3:158430706-158828643	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv1001450	chr3:158440011-158768399	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv536777	chr3:158440011-158768399	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4264773	RARRES1	cis	cerebellum	SCAN
rs4264773	LXN	cis	parietal	SCAN
rs4264773	LXN	cis	cerebellum	SCAN
rs4264773	GFM1	Cis_1M	lymphoblastoid	RTeQTL
rs4264773	MLF1	cis	lymphoblastoid	seeQTL

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158449800-158483000	Weak transcription	Fetal Heart	heart
2	chr3:158450600-158465400	Weak transcription	Left Ventricle	heart
3	chr3:158450800-158464200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr3:158450800-158468000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:158450800-158485400	Weak transcription	Psoas Muscle	Psoas
6	chr3:158451000-158463400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:158451000-158463800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr3:158451000-158464000	Weak transcription	Colonic Mucosa	Colon
9	chr3:158451000-158464400	Weak transcription	NH-A	brain
10	chr3:158451000-158464800	Weak transcription	Gastric	stomach
11	chr3:158451000-158484200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr3:158451000-158485800	Weak transcription	Fetal Kidney	kidney
13	chr3:158451800-158464800	Weak transcription	Brain Germinal Matrix	brain
14	chr3:158452200-158465600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr3:158453200-158464600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr3:158453400-158464200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:158453400-158464800	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr3:158453400-158465800	Weak transcription	Fetal Brain Female	brain
19	chr3:158453400-158467400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:158453400-158467600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:158453600-158464000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr3:158453600-158465400	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr3:158453600-158486400	Weak transcription	Esophagus	oesophagus
24	chr3:158455400-158465800	Weak transcription	Brain Cingulate Gyrus	brain
25	chr3:158456800-158464800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:158457000-158464600	Weak transcription	HSMM	muscle
27	chr3:158457200-158464800	Weak transcription	Spleen	Spleen
28	chr3:158457200-158468200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr3:158457400-158486000	Weak transcription	Right Ventricle	heart
30	chr3:158457800-158464800	Weak transcription	Hela-S3	cervix
31	chr3:158457800-158466000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr3:158457800-158486200	Weak transcription	Pancreas	Pancrea
33	chr3:158458000-158464800	Weak transcription	HSMMtube	muscle
34	chr3:158458000-158471200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr3:158458800-158464600	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr3:158459400-158464800	Weak transcription	Brain Angular Gyrus	brain
37	chr3:158459600-158465000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr3:158459600-158465600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr3:158459600-158468400	Strong transcription	Fetal Muscle Trunk	muscle
40	chr3:158460000-158468600	Strong transcription	Fetal Intestine Large	intestine
41	chr3:158460200-158466600	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr3:158460400-158464600	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr3:158460400-158465800	Weak transcription	Lung	lung
44	chr3:158460400-158486000	Weak transcription	Brain Hippocampus Middle	brain
45	chr3:158460600-158465600	Weak transcription	Aorta	Aorta
46	chr3:158460800-158469400	Weak transcription	Ovary	ovary
47	chr3:158461000-158464200	Weak transcription	A549	lung
48	chr3:158461000-158464800	Weak transcription	Liver	Liver
49	chr3:158461200-158464800	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr3:158461400-158464200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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