Variant report

Variant	rs4897484
Chromosome Location	chr6:131338166-131338167
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	FOXA1	chr6:131337916-131338194	HepG2	liver:	n/a	chr6:131338104-131338119 chr6:131338020-131338032
2	FOXA2	chr6:131337782-131338216	A549	lung:	n/a	chr6:131338020-131338032
3	KAP1	chr6:131337832-131338268	HEK293	kidney:	n/a	n/a
4	KAP1	chr6:131337749-131338549	U2OS	brain:	n/a	n/a
5	SETDB1	chr6:131337782-131338204	U2OS	brain:	n/a	n/a

Variant related genes	Relation type
EPB41L2	TF binding region

Extended variants
information (count: 90 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs12525104	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12525986	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13437326	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17178878	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17179123	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17180687	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17180867	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17770255	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs17784418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17784472	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17784896	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17785507	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1811949	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1977576	0.95[ASN][1000 genomes]
rs2095961	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2183967	0.88[CEU][hapmap]
rs2297853	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs28482889	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34899420	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3777434	0.88[CEU][hapmap]
rs3777435	0.88[CEU][hapmap]
rs3777436	0.88[CEU][hapmap]
rs3777440	0.90[MKK][hapmap]
rs3777442	0.86[MKK][hapmap]
rs3777461	0.90[MKK][hapmap]
rs3777466	0.88[MKK][hapmap]
rs3822863	0.86[MKK][hapmap]
rs4895901	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4895903	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4895904	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4895906	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4895907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4895908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4895909	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4897468	0.84[CEU][hapmap]
rs4897473	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.82[TSI][hapmap]
rs4897477	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4897478	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4897483	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4897485	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4897486	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4897487	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4897489	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4897491	1.00[ASN][1000 genomes]
rs55898152	1.00[ASN][1000 genomes]
rs56163502	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56173113	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56201801	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58503799	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62422362	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62422365	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62422380	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62423581	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62423597	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62423598	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6569707	0.88[CEU][hapmap]
rs6569708	0.85[CEU][hapmap]
rs6906059	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6906478	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs6916024	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6919007	0.85[CEU][hapmap]
rs6921396	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6922045	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6922177	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6926250	0.87[CEU][hapmap];1.00[CHB][hapmap]
rs6928920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6931804	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs6935108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7741148	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7755720	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7758016	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7760965	0.84[CEU][hapmap]
rs7761311	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7769678	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7771543	0.89[ASN][1000 genomes]
rs7775013	0.88[CEU][hapmap]
rs872576	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9321263	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs9372985	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs9385568	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9388861	0.90[CEU][hapmap]
rs9388863	0.88[CEU][hapmap]
rs9402292	0.81[CEU][hapmap]
rs9402299	0.86[MKK][hapmap]
rs9402303	0.89[ASN][1000 genomes]
rs942	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9483206	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs954211	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[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	nsv1032955	chr6:131298803-131818502	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv538443	chr6:131298803-131818502	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4897484	PSMD3	trans	cerebellum	SCAN
rs4897484	EPB41L2	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:131329800-131347400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr6:131332200-131345400	Weak transcription	Left Ventricle	heart
3	chr6:131332800-131339600	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr6:131333600-131339200	Weak transcription	Pancreas	Pancrea
5	chr6:131334600-131338200	Enhancers	HepG2	liver
6	chr6:131334600-131338200	Enhancers	Osteobl	bone
7	chr6:131334600-131339000	Enhancers	Rectal Smooth Muscle	rectum
8	chr6:131334800-131342800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:131335200-131343200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr6:131335400-131338200	Enhancers	Colon Smooth Muscle	Colon
11	chr6:131335600-131345200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr6:131336000-131338200	Enhancers	Stomach Smooth Muscle	stomach
13	chr6:131336600-131345200	Weak transcription	Ovary	ovary
14	chr6:131337000-131338800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr6:131337200-131338200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr6:131337200-131338400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr6:131337200-131345000	Weak transcription	Hela-S3	cervix
18	chr6:131337200-131345000	Weak transcription	NHLF	lung
19	chr6:131337400-131338200	Enhancers	Brain Anterior Caudate	brain
20	chr6:131337400-131339000	Weak transcription	Brain Angular Gyrus	brain
21	chr6:131337400-131339600	Weak transcription	HMEC	breast
22	chr6:131337400-131347200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr6:131337600-131345200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr6:131337800-131339200	Weak transcription	Brain Substantia Nigra	brain
25	chr6:131337800-131345000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr6:131337800-131345000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr6:131337800-131345200	Weak transcription	Brain Cingulate Gyrus	brain
28	chr6:131337800-131345400	Weak transcription	Right Atrium	heart
29	chr6:131337800-131351000	Weak transcription	Stomach Mucosa	stomach
30	chr6:131338000-131339000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr6:131338000-131339200	Weak transcription	Gastric	stomach
32	chr6:131338000-131339400	Weak transcription	Fetal Muscle Leg	muscle
33	chr6:131338000-131339600	Enhancers	A549	lung
34	chr6:131338000-131345000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr6:131338000-131345000	Weak transcription	Brain Hippocampus Middle	brain
36	chr6:131338000-131345000	Weak transcription	NHDF-Ad	bronchial
37	chr6:131338000-131345200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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