Variant report

Variant	rs3843493
Chromosome Location	chr5:107141308-107141309
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:107139921..107141469-chr5:107142790..107144472,2	K562	blood:
2	chr5:107125029..107126613-chr5:107139861..107141985,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10066422	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11747409	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11748620	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2410957	1.00[CEU][hapmap];0.92[CHB][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2410958	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2410959	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2898606	0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3846692	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3846693	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3909362	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3910210	0.81[ASN][1000 genomes]
rs3931059	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3931060	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3931725	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4099186	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4099187	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4099188	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4099189	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4100173	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4957541	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4957721	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4957722	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55976515	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6596749	1.00[CEU][hapmap];0.92[CHB][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6596750	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6596751	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6860214	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6860370	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6860400	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6860649	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6861427	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6866321	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6867170	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6867698	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6868088	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6870561	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6871212	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6871231	1.00[CEU][hapmap];0.92[CHB][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6875432	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6876427	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6879536	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6879852	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6880537	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6882183	1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6885982	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6888461	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6889417	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6892119	1.00[CEU][hapmap];0.82[CHB][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6892137	1.00[CEU][hapmap];0.92[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6893393	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6895001	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7702274	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv969928	chr5:107132237-107143800	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3843493	WDR36	cis	cerebellum	SCAN
rs3843493	CAMK4	cis	cerebellum	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:107135400-107143000	Weak transcription	Right Atrium	heart
2	chr5:107135800-107141400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr5:107137800-107141400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr5:107138400-107144800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:107139800-107142000	Weak transcription	NHDF-Ad	bronchial
6	chr5:107140200-107144200	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr5:107140200-107144400	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr5:107140400-107141400	Enhancers	Fetal Intestine Large	intestine
9	chr5:107140400-107144000	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr5:107140400-107144000	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr5:107140400-107144200	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr5:107140400-107148800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr5:107140600-107142800	Enhancers	H9 Cell Line	embryonic stem cell
14	chr5:107140600-107144000	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr5:107140800-107141600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
16	chr5:107140800-107142400	Enhancers	Brain Germinal Matrix	brain
17	chr5:107140800-107142800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr5:107140800-107144400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr5:107140800-107145000	Enhancers	H1 Cell Line	embryonic stem cell
20	chr5:107140800-107146600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr5:107141000-107141400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
22	chr5:107141000-107142000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr5:107141000-107142800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:107141000-107143800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr5:107141200-107142200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr5:107141200-107144400	Weak transcription	Dnd41	blood

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