Variant report

Variant	rs1530298
Chromosome Location	chr4:77202882-77202883
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:77202480..77205980-chr4:77226274..77229049,3	MCF-7	breast:
2	chr4:77068994..77070621-chr4:77200458..77203318,2	K562	blood:

Variant related genes	Relation type
ENSG00000118804	Chromatin interaction
ENSG00000138750	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1036788	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs11097313	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11097314	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11097320	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs11933305	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11934863	1.00[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11946806	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12643334	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13119644	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13123108	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13151765	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1441909	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1441910	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1441913	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1441914	1.00[CEU][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1441916	0.82[ASN][1000 genomes]
rs1530295	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs1530296	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1530297	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1583944	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17236158	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17308336	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1876536	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1876537	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1876538	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1876539	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1876540	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1876541	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1876542	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1876543	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1969148	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1969149	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2869870	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2869871	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3733250	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3733253	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3821980	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4370157	0.81[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs4859439	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4859440	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4859441	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4859650	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4859651	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4859654	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4859655	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4859656	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4859657	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4859658	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs59864739	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60397621	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60876302	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61595008	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6823078	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs736634	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs736636	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7665023	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs768979	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7699714	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs964051	1.00[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv461559	chr4:77192838-77204500	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv594695	chr4:77192838-77204500	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1530298	FAM47E	cis	Thyroid	GTEx

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:77173800-77215800	Weak transcription	Brain Hippocampus Middle	brain
2	chr4:77186400-77204200	Weak transcription	Aorta	Aorta
3	chr4:77186600-77215000	Weak transcription	Brain Anterior Caudate	brain
4	chr4:77192600-77212200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr4:77194000-77204200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr4:77194200-77216400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr4:77199800-77203600	Enhancers	Liver	Liver
8	chr4:77199800-77204200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr4:77200800-77203000	Enhancers	Stomach Mucosa	stomach
10	chr4:77201400-77203000	Enhancers	Adipose Nuclei	Adipose
11	chr4:77201400-77203000	Enhancers	Duodenum Mucosa	Duodenum
12	chr4:77201400-77203000	Enhancers	HepG2	liver
13	chr4:77201400-77203600	Enhancers	Primary neutrophils fromperipheralblood	blood
14	chr4:77201400-77204400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr4:77201400-77205800	Enhancers	Fetal Intestine Large	intestine
16	chr4:77201600-77203000	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr4:77201600-77204600	Enhancers	Fetal Heart	heart
18	chr4:77202400-77203600	Weak transcription	Placenta	Placenta
19	chr4:77202400-77203600	Weak transcription	Gastric	stomach
20	chr4:77202400-77204200	Weak transcription	Colonic Mucosa	Colon
21	chr4:77202400-77204200	Weak transcription	Right Atrium	heart
22	chr4:77202400-77204200	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr4:77202400-77205000	Weak transcription	Pancreas	Pancrea
24	chr4:77202400-77206200	Weak transcription	Psoas Muscle	Psoas
25	chr4:77202400-77217000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr4:77202400-77221000	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr4:77202600-77204200	Weak transcription	Fetal Intestine Small	intestine
28	chr4:77202600-77204200	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr4:77202800-77203000	Enhancers	Brain Substantia Nigra	brain

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