Variant report

Variant	rs202456
Chromosome Location	chr20:1714362-1714363
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs202457	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs202459	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs202461	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs202462	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs202463	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs202466	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs202467	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs202500	0.83[AFR][1000 genomes]
rs202503	0.87[AFR][1000 genomes]
rs202507	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs202508	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs202509	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs202510	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs202514	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs202515	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs202518	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs517578	1.00[ASW][hapmap];0.84[TSI][hapmap];0.84[YRI][hapmap]
rs599837	0.84[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv585206	chr20:1386473-1714362	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv912596	chr20:1486637-1877150	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv1057036	chr20:1493425-1869281	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv912597	chr20:1500506-1877150	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv833894	chr20:1519433-1753366	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv531473	chr20:1532476-1864506	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	nsv962538	chr20:1702183-1716952	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs202456	STK35	cis	cerebellum	SCAN
rs202456	FAM113A	cis	parietal	SCAN
rs202456	SRXN1	cis	cerebellum	SCAN
rs202456	SCRT2	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1701400-1714600	Weak transcription	Brain Hippocampus Middle	brain
2	chr20:1703400-1720200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr20:1710600-1714800	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr20:1710800-1714800	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr20:1711800-1715000	Enhancers	GM12878-XiMat	blood
6	chr20:1712800-1714400	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr20:1712800-1714800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr20:1712800-1715400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr20:1712800-1715400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr20:1712800-1719400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr20:1713000-1714800	Weak transcription	Thymus	Thymus
12	chr20:1713000-1715400	Enhancers	Primary T cells from cord blood	blood
13	chr20:1713000-1715400	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr20:1713200-1714600	Weak transcription	Duodenum Mucosa	Duodenum
15	chr20:1713200-1715200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr20:1713200-1715600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
17	chr20:1713400-1714400	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr20:1713400-1714800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr20:1713400-1714800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr20:1713400-1714800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr20:1713400-1714800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr20:1713400-1714800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr20:1713400-1714800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr20:1714000-1714800	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr20:1714200-1715600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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