Variant report

Variant	rs6788069
Chromosome Location	chr3:158459459-158459460
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:158458577..158461138-chr3:158482458..158485038,2	MCF-7	breast:
2	chr3:158458110..158459848-chr3:158463726..158465479,2	K562	blood:
3	chr3:158458014..158460479-chr3:158462665..158465374,2	MCF-7	breast:
4	chr3:158450628..158453844-chr3:158458339..158460802,3	MCF-7	breast:
5	chr3:158449518..158452301-chr3:158459445..158461746,2	K562	blood:

Variant related genes	Relation type
ENSG00000118849	Chromatin interaction
ENSG00000118855	Chromatin interaction
ENSG00000240207	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10513527	0.87[GIH][hapmap]
rs16829118	0.87[GIH][hapmap]
rs16847130	0.84[GIH][hapmap]
rs16847135	0.87[GIH][hapmap]
rs17630223	0.86[GIH][hapmap]
rs17630394	0.84[GIH][hapmap]
rs2082838	0.87[GIH][hapmap]
rs2291594	0.87[GIH][hapmap]
rs3806642	0.87[GIH][hapmap]
rs4264773	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs55835802	0.86[ASN][1000 genomes]
rs58152433	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59192661	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59217052	1.00[ASN][1000 genomes]
rs59313096	1.00[ASN][1000 genomes]
rs59918529	1.00[ASN][1000 genomes]
rs59957986	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61080878	0.86[ASN][1000 genomes]
rs61387735	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61558956	1.00[ASN][1000 genomes]
rs61696028	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441222	1.00[ASN][1000 genomes]
rs67301795	0.86[ASN][1000 genomes]
rs67305172	0.86[ASN][1000 genomes]
rs67446837	0.86[ASN][1000 genomes]
rs6775607	0.86[ASN][1000 genomes]
rs73015629	0.98[EUR][1000 genomes]
rs73015644	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73015651	1.00[ASN][1000 genomes]
rs73015652	1.00[ASN][1000 genomes]
rs73015654	1.00[ASN][1000 genomes]
rs73015655	1.00[ASN][1000 genomes]
rs73015657	1.00[ASN][1000 genomes]
rs73015665	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73015669	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73017536	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73017539	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73017540	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73017541	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73158333	0.86[ASN][1000 genomes]
rs73158334	0.86[ASN][1000 genomes]
rs7617304	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[ASN][1000 genomes]
rs7624161	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7635704	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7636023	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638518	0.81[GIH][hapmap]
rs7646881	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs7646987	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs9864589	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6788069	RARRES1	cis	cerebellum	SCAN
rs6788069	RARRES1	cis	multi-tissue	Pritchard

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158449800-158483000	Weak transcription	Fetal Heart	heart
2	chr3:158450400-158460000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr3:158450600-158465400	Weak transcription	Left Ventricle	heart
4	chr3:158450800-158460800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:158450800-158464200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr3:158450800-158468000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:158450800-158485400	Weak transcription	Psoas Muscle	Psoas
8	chr3:158451000-158459800	Weak transcription	Fetal Brain Male	brain
9	chr3:158451000-158459800	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr3:158451000-158460000	Weak transcription	Fetal Intestine Large	intestine
11	chr3:158451000-158462000	Weak transcription	Colon Smooth Muscle	Colon
12	chr3:158451000-158463400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr3:158451000-158463800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr3:158451000-158464000	Weak transcription	Colonic Mucosa	Colon
15	chr3:158451000-158464400	Weak transcription	NH-A	brain
16	chr3:158451000-158464800	Weak transcription	Gastric	stomach
17	chr3:158451000-158484200	Weak transcription	Rectal Smooth Muscle	rectum
18	chr3:158451000-158485800	Weak transcription	Fetal Kidney	kidney
19	chr3:158451800-158461400	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr3:158451800-158464800	Weak transcription	Brain Germinal Matrix	brain
21	chr3:158452200-158465600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr3:158453200-158459800	Weak transcription	Ovary	ovary
23	chr3:158453200-158462000	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr3:158453200-158464600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr3:158453400-158460800	Strong transcription	Stomach Smooth Muscle	stomach
26	chr3:158453400-158462800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr3:158453400-158464200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr3:158453400-158464800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr3:158453400-158465800	Weak transcription	Fetal Brain Female	brain
30	chr3:158453400-158467400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr3:158453400-158467600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr3:158453600-158459600	Weak transcription	Primary T cells from cord blood	blood
33	chr3:158453600-158462000	Weak transcription	Brain Anterior Caudate	brain
34	chr3:158453600-158462600	Weak transcription	Brain Substantia Nigra	brain
35	chr3:158453600-158464000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr3:158453600-158465400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr3:158453600-158486400	Weak transcription	Esophagus	oesophagus
38	chr3:158454000-158460800	Weak transcription	A549	lung
39	chr3:158455400-158465800	Weak transcription	Brain Cingulate Gyrus	brain
40	chr3:158455800-158460800	Strong transcription	Fetal Stomach	stomach
41	chr3:158456400-158460400	Weak transcription	Placenta	Placenta
42	chr3:158456400-158461600	Weak transcription	Osteobl	bone
43	chr3:158456600-158459800	Weak transcription	Liver	Liver
44	chr3:158456800-158464800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr3:158457000-158459800	Weak transcription	NHLF	lung
46	chr3:158457000-158464600	Weak transcription	HSMM	muscle
47	chr3:158457200-158459800	Weak transcription	Fetal Lung	lung
48	chr3:158457200-158459800	Enhancers	K562	blood
49	chr3:158457200-158460200	Weak transcription	Lung	lung
50	chr3:158457200-158464800	Weak transcription	Spleen	Spleen

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