Variant report

Variant	rs1441914
Chromosome Location	chr4:77196500-77196501
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr4:77196269-77197336	HepG2	liver:	n/a	n/a
2	MYBL2	chr4:77196332-77197136	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
FAM47E	TF binding region

Extended variants
information (count: 85 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs11097313	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11097314	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11531413	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs11933305	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11934863	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11946806	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12643261	0.85[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs12643334	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12651582	0.85[CHB][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs13117238	0.81[JPT][hapmap]
rs13119644	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13122345	0.94[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs13123108	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13136819	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs13137733	0.84[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs13151765	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1441909	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1441910	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1441913	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1530296	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1530298	1.00[CEU][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1583943	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs1583944	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1588214	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs1596115	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs1596116	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs17236158	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17308336	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1876536	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1876537	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1876538	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1876539	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1876540	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1876541	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1876542	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1876543	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1969148	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1969149	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2119731	0.88[JPT][hapmap]
rs2289514	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2869863	0.86[ASN][1000 genomes]
rs2869864	0.84[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs2869870	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2869871	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34638846	0.86[ASN][1000 genomes]
rs3733250	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3733253	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3821980	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859437	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs4859439	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4859440	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4859441	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4859641	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs4859643	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs4859648	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs4859650	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4859651	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4859652	0.84[ASN][1000 genomes]
rs4859653	0.86[ASN][1000 genomes]
rs4859654	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859655	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859656	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859657	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56060342	0.84[ASN][1000 genomes]
rs58804635	0.84[ASN][1000 genomes]
rs59864739	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60397621	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60876302	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61595008	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6813980	0.81[JPT][hapmap]
rs6823078	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6846983	0.81[JPT][hapmap]
rs6849069	0.81[JPT][hapmap]
rs6851219	0.85[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs71607346	0.86[ASN][1000 genomes]
rs736634	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs736636	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7665023	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7677256	0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs7687964	0.84[ASN][1000 genomes]
rs768979	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7699714	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs964051	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][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
rs1441914	FAM47E	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:77173600-77202000	Weak transcription	Psoas Muscle	Psoas
2	chr4:77173800-77215800	Weak transcription	Brain Hippocampus Middle	brain
3	chr4:77177800-77199200	Weak transcription	Placenta	Placenta
4	chr4:77178800-77201200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr4:77180000-77202000	Weak transcription	Gastric	stomach
6	chr4:77186400-77204200	Weak transcription	Aorta	Aorta
7	chr4:77186600-77196800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr4:77186600-77215000	Weak transcription	Brain Anterior Caudate	brain
9	chr4:77187600-77202000	Weak transcription	Brain Substantia Nigra	brain
10	chr4:77188000-77202200	Weak transcription	Brain Angular Gyrus	brain
11	chr4:77188200-77202000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr4:77190400-77199200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr4:77191800-77199400	Enhancers	Liver	Liver
14	chr4:77192600-77212200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr4:77192800-77197200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr4:77193000-77201800	Weak transcription	Left Ventricle	heart
17	chr4:77193000-77202000	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr4:77193000-77202200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr4:77194000-77204200	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr4:77194200-77216400	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr4:77195000-77200200	Enhancers	HepG2	liver
22	chr4:77195200-77197000	Enhancers	Stomach Mucosa	stomach
23	chr4:77195400-77199400	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr4:77195800-77196600	Enhancers	Rectal Mucosa Donor 29	rectum
25	chr4:77195800-77200400	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr4:77196000-77197000	Enhancers	Fetal Intestine Small	intestine
27	chr4:77196200-77196600	Enhancers	Fetal Intestine Large	intestine
28	chr4:77196200-77199600	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr4:77196400-77198000	Weak transcription	Adipose Nuclei	Adipose

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