Variant report

Variant	rs3852618
Chromosome Location	chr13:37681126-37681127
allele	C/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	USF1	chr13:37680851-37681142	H1-hESC	embryonic stem cell:	n/a	n/a
2	USF1	chr13:37680797-37681264	H1-hESC	embryonic stem cell:	n/a	n/a
3	USF2	chr13:37680887-37681131	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAX	chr13:37680791-37681169	H1-hESC	embryonic stem cell:	n/a	n/a
5	E2F6	chr13:37680782-37681277	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
CSNK1A1L	TF binding region

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1009963	0.89[ASN][1000 genomes]
rs11147624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11147625	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11147626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11147627	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11147629	0.91[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11147630	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11147632	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11620134	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1199995	0.93[ASN][1000 genomes]
rs1199996	0.93[ASN][1000 genomes]
rs12583685	0.90[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12584417	0.91[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12585998	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1336754	0.97[AFR][1000 genomes]
rs1336762	0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs1764480	0.91[ASN][1000 genomes]
rs1781669	0.94[ASN][1000 genomes]
rs1781670	0.94[ASN][1000 genomes]
rs1856028	0.96[YRI][hapmap];0.97[AFR][1000 genomes]
rs1856029	0.92[ASN][1000 genomes]
rs1937757	0.87[AFR][1000 genomes]
rs2078022	0.86[JPT][hapmap]
rs2243710	0.86[JPT][hapmap]
rs2323396	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2670061	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3818380	0.86[JPT][hapmap]
rs3852619	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3852620	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3864999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3888918	0.92[ASN][1000 genomes]
rs3904095	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3904755	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3914300	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4054546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4485226	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4943440	0.86[JPT][hapmap]
rs6563510	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6563511	0.81[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs7327617	0.94[ASN][1000 genomes]
rs7335490	0.93[AFR][1000 genomes]
rs7981360	0.93[ASN][1000 genomes]
rs7996099	0.88[AFR][1000 genomes]
rs7996605	0.93[ASN][1000 genomes]
rs7996662	0.93[ASN][1000 genomes]
rs8000946	0.86[JPT][hapmap]
rs8002580	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8003010	0.93[ASN][1000 genomes]
rs945632	0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs954370	0.86[JPT][hapmap]
rs9547711	0.86[JPT][hapmap]
rs9547713	0.86[JPT][hapmap]
rs9566176	0.82[AFR][1000 genomes]
rs9566177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9566178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9566183	0.94[ASN][1000 genomes]
rs9566184	0.94[ASN][1000 genomes]
rs9566185	0.93[ASN][1000 genomes]
rs9566186	0.93[ASN][1000 genomes]
rs9576151	0.86[JPT][hapmap]
rs9576167	0.85[JPT][hapmap]
rs9576172	0.82[AFR][1000 genomes]
rs9576173	0.83[AFR][1000 genomes]
rs9576175	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576176	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576177	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9576178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576180	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9576181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576182	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576183	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576184	1.00[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9576185	0.82[ASN][1000 genomes]
rs9576186	0.93[ASN][1000 genomes]
rs9576187	0.93[ASN][1000 genomes]
rs9603126	0.86[JPT][hapmap]
rs9603139	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv948975	chr13:37281203-38280430	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	esv12579	chr13:37679949-37681397	Enhancers Weak transcription Strong transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:37677800-37682200	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr13:37679800-37681800	Weak transcription	Spleen	Spleen
3	chr13:37679800-37682800	Weak transcription	Fetal Stomach	stomach
4	chr13:37680200-37681600	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr13:37680200-37682000	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr13:37680400-37681400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr13:37680400-37681400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr13:37680400-37681400	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr13:37680400-37681600	Enhancers	Colon Smooth Muscle	Colon
10	chr13:37680400-37682000	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr13:37680400-37682000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr13:37680400-37682600	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr13:37680600-37681200	Enhancers	H1 Cell Line	embryonic stem cell
14	chr13:37680600-37681200	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr13:37680600-37681200	Enhancers	Muscle Satellite Cultured Cells	--
16	chr13:37680600-37681400	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr13:37680600-37681800	Enhancers	H9 Cell Line	embryonic stem cell
18	chr13:37680600-37682000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr13:37680800-37681200	Enhancers	Fetal Kidney	kidney
20	chr13:37681000-37681400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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