Variant report

Variant	rs6823078
Chromosome Location	chr4:77196848-77196849
allele	A/G
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	chr4:77196600-77196944	A549	lung:	n/a	n/a
2	JUN	chr4:77196588-77196981	HepG2	liver:	n/a	chr4:77196759-77196772
3	REST	chr4:77196638-77196979	HepG2	liver:	n/a	n/a
4	RCOR1	chr4:77196644-77196894	HepG2	liver:	n/a	n/a
5	FOXA2	chr4:77196630-77197008	HepG2	liver:	n/a	n/a
6	CEBPB	chr4:77196817-77197281	A549	lung:	n/a	chr4:77197056-77197067
7	MXI1	chr4:77196669-77197186	HepG2	liver:	n/a	n/a
8	FOXA1	chr4:77196544-77197126	HepG2	liver:	n/a	n/a
9	SP1	chr4:77196612-77197044	HepG2	liver:	n/a	n/a
10	FOXA2	chr4:77196269-77197336	HepG2	liver:	n/a	n/a
11	MAFF	chr4:77196698-77197071	HepG2	liver:	n/a	n/a
12	FOXA1	chr4:77196544-77197097	HepG2	liver:	n/a	n/a
13	MAX	chr4:77196727-77196935	HepG2	liver:	n/a	n/a
14	CEBPB	chr4:77196842-77197203	MCF-7	breast:	n/a	chr4:77197056-77197067
15	ARID3A	chr4:77196531-77197258	HepG2	liver:	n/a	n/a
16	EP300	chr4:77196501-77197089	HepG2	liver:	n/a	n/a
17	CEBPB	chr4:77196679-77196861	HepG2	liver:	n/a	n/a
18	BHLHE40	chr4:77196655-77197263	HepG2	liver:	n/a	n/a
19	CEBPB	chr4:77196749-77197234	A549	lung:	n/a	chr4:77197056-77197067
20	FOSL2	chr4:77196600-77197034	HepG2	liver:	n/a	n/a
21	JUND	chr4:77196584-77196968	HepG2	liver:	n/a	n/a
22	HNF4A	chr4:77196688-77196925	HepG2	liver:	n/a	n/a
23	NFIC	chr4:77196534-77197067	HepG2	liver:	n/a	n/a
24	JUND	chr4:77196596-77197047	HepG2	liver:	n/a	n/a
25	RXRA	chr4:77196625-77196924	HepG2	liver:	n/a	n/a
26	MBD4	chr4:77196523-77197067	HepG2	liver:	n/a	n/a
27	FOXA1	chr4:77196719-77196921	T-47D	breast:	n/a	n/a
28	SMC3	chr4:77196747-77197308	HepG2	liver:	n/a	n/a
29	FOXA1	chr4:77196547-77197030	HepG2	liver:	n/a	n/a
30	MYBL2	chr4:77196332-77197136	HepG2	liver:	n/a	n/a
31	CEBPB	chr4:77196657-77197239	HepG2	liver:	n/a	chr4:77197056-77197067
32	MAFK	chr4:77196746-77196951	HepG2	liver:	n/a	n/a
33	FOXA1	chr4:77196606-77197160	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
FAM47E	TF binding region

Extended variants
information (count: 85 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11097313	0.85[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11097314	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11531413	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs11933305	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11934863	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11946806	0.92[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];0.93[YRI][hapmap];1.00[AFR][1000 genomes];0.99[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	1.00[AFR][1000 genomes];0.99[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	0.97[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	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1441909	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1441910	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1441913	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1441914	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]
rs1530296	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1530298	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1583943	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs1583944	1.00[AFR][1000 genomes];0.99[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];0.95[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];0.84[YRI][hapmap];0.85[AFR][1000 genomes];0.98[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];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1876537	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1876538	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1876539	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1876540	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1876541	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1876542	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1876543	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1969148	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1969149	0.89[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	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2869871	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34638846	0.86[ASN][1000 genomes]
rs3733250	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3733253	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3821980	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859437	0.80[CHB][hapmap];0.81[JPT][hapmap]
rs4859439	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4859440	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4859441	0.92[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	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4859651	0.91[AFR][1000 genomes];0.98[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	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859655	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859656	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4859657	0.91[AFR][1000 genomes];0.98[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	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60397621	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60876302	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61595008	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6813980	0.81[JPT][hapmap]
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	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs736636	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7665023	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7677256	0.90[CHD][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs7687964	0.84[ASN][1000 genomes]
rs768979	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7699714	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs964051	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6823078	FAM47E	cis	cerebellum	SCAN
rs6823078	FAM47E	cis	Thyroid	GTEx
rs6823078	CCDC158	cis	parietal	SCAN
rs6823078	FAM47E	cis	parietal	SCAN

Chromatin state (count:31 , 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	chr4:77186600-77215000	Weak transcription	Brain Anterior Caudate	brain
8	chr4:77187600-77202000	Weak transcription	Brain Substantia Nigra	brain
9	chr4:77188000-77202200	Weak transcription	Brain Angular Gyrus	brain
10	chr4:77188200-77202000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr4:77190400-77199200	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr4:77191800-77199400	Enhancers	Liver	Liver
13	chr4:77192600-77212200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr4:77192800-77197200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr4:77193000-77201800	Weak transcription	Left Ventricle	heart
16	chr4:77193000-77202000	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr4:77193000-77202200	Weak transcription	Brain Cingulate Gyrus	brain
18	chr4:77194000-77204200	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr4:77194200-77216400	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr4:77195000-77200200	Enhancers	HepG2	liver
21	chr4:77195200-77197000	Enhancers	Stomach Mucosa	stomach
22	chr4:77195400-77199400	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr4:77195800-77200400	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr4:77196000-77197000	Enhancers	Fetal Intestine Small	intestine
25	chr4:77196200-77199600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr4:77196400-77198000	Weak transcription	Adipose Nuclei	Adipose
27	chr4:77196600-77199000	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr4:77196600-77199400	Weak transcription	Fetal Intestine Large	intestine
29	chr4:77196800-77197000	Enhancers	Duodenum Mucosa	Duodenum
30	chr4:77196800-77197200	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr4:77196800-77198200	Enhancers	Primary hematopoietic stem cells short term culture	blood

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