Variant report

Variant	rs6882183
Chromosome Location	chr5:107145253-107145254
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	BACH1	chr5:107144783-107145397	H1-hESC	embryonic stem cell:	n/a	n/a
2	TCF12	chr5:107145234-107145674	H1-hESC	embryonic stem cell:	n/a	n/a
3	FOS	chr5:107145209-107145551	MCF10A-Er-Src	breast:	n/a	n/a
4	HDAC2	chr5:107144386-107145282	H1-hESC	embryonic stem cell:	n/a	chr5:107144961-107144975 chr5:107144966-107144980 chr5:107144969-107144983
5	TEAD4	chr5:107145250-107145775	H1-hESC	embryonic stem cell:	n/a	n/a
6	KAP1	chr5:107145093-107145537	U2OS	brain:	n/a	n/a

Variant related genes	Relation type
RN7SKP122	TF binding region

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

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

rs_ID	r²[population]
rs10066422	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11742684	0.81[ASN][1000 genomes]
rs11747409	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11748620	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2033479	0.84[AMR][1000 genomes]
rs2410957	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2410958	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2410959	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2898606	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34695771	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3843493	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3846692	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3846693	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3909359	0.87[ASN][1000 genomes]
rs3909360	0.87[ASN][1000 genomes]
rs3909362	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3931059	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3931060	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3931725	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4099186	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4099187	1.00[CEU][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4099188	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4099189	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4100173	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4957541	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4957721	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4957722	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55976515	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6596749	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6596750	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6596751	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6596754	0.82[ASN][1000 genomes]
rs6596755	0.84[ASN][1000 genomes]
rs6860214	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6860370	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6860400	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6860649	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6861427	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6866321	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6867170	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6867698	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6868088	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6870561	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6871212	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6871231	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6875432	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6876427	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6879536	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6879852	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6880537	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6885982	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6888461	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6889417	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6892119	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6892137	1.00[CEU][hapmap];0.97[GIH][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6893393	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6895001	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7702274	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7704143	0.90[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	nsv830440	chr5:107074116-107278905	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1022155	chr5:107138981-107149604	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6882183	CAMK4	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:107140400-107148800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
2	chr5:107140800-107146600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr5:107141400-107146000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr5:107141400-107146600	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr5:107142600-107145400	Enhancers	Fetal Kidney	kidney
6	chr5:107143000-107148000	Weak transcription	HSMM	muscle
7	chr5:107143600-107145800	Weak transcription	Fetal Heart	heart
8	chr5:107143600-107148000	Weak transcription	HSMMtube	muscle
9	chr5:107143800-107145800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
10	chr5:107144000-107145800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr5:107144000-107145800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
12	chr5:107144000-107146200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:107144000-107146600	Enhancers	H9 Cell Line	embryonic stem cell
14	chr5:107144200-107145600	Enhancers	Fetal Stomach	stomach
15	chr5:107144200-107145800	Enhancers	NH-A	brain
16	chr5:107144400-107145600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr5:107144400-107146200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr5:107144400-107167600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr5:107144600-107145400	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr5:107144600-107145600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr5:107144600-107145800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr5:107144600-107145800	Enhancers	NHDF-Ad	bronchial
23	chr5:107144800-107145600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr5:107144800-107145800	Enhancers	Muscle Satellite Cultured Cells	--
25	chr5:107144800-107146000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr5:107144800-107147600	Weak transcription	Fetal Muscle Leg	muscle
27	chr5:107144800-107148400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr5:107144800-107150200	Weak transcription	Right Atrium	heart
29	chr5:107145000-107145400	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr5:107145000-107145600	Enhancers	Fetal Lung	lung
31	chr5:107145000-107145600	Enhancers	NHLF	lung
32	chr5:107145000-107146000	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr5:107145000-107146000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
34	chr5:107145000-107148000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr5:107145200-107145400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr5:107145200-107145400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
37	chr5:107145200-107145800	Enhancers	Hela-S3	cervix
38	chr5:107145200-107146200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr5:107145200-107146600	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr5:107145200-107148000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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