Variant report

Variant	rs1540299
Chromosome Location	chr22:33907964-33907965
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11704444	0.81[JPT][hapmap]
rs11704460	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs1807492	0.95[CEU][hapmap];0.91[CHB][hapmap]
rs2267221	0.92[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap]
rs2267222	0.92[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap]
rs2267223	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2267225	0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs2267226	0.95[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs2267227	0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs2899209	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4820107	0.81[JPT][hapmap]
rs4821157	0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs4821158	0.95[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs5749623	0.91[CHB][hapmap]
rs5749624	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs5754581	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5754585	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs5754588	0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs5754589	0.95[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs5754590	1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs5754591	0.89[ASN][1000 genomes]
rs5754592	0.95[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs5754594	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs5754596	0.82[CHB][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap]
rs5754601	0.90[GIH][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap]
rs5998999	0.95[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs7289066	0.85[JPT][hapmap]
rs739027	1.00[YRI][hapmap];0.86[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:34 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948523	chr22:33414164-34098417	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	nsv933455	chr22:33532697-33915429	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	nsv934109	chr22:33722066-34339500	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1062127	chr22:33755479-34085278	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
5	nsv544683	chr22:33755479-34085278	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
6	nsv531588	chr22:33776857-34150188	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
7	nsv914983	chr22:33800119-34035034	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
8	nsv1060283	chr22:33809137-34043739	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
9	nsv544684	chr22:33809137-34043739	Weak transcription ZNF genes & repeats Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
10	nsv1057547	chr22:33810445-33939474	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
11	nsv1055791	chr22:33822226-34159536	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
12	nsv1065417	chr22:33823850-34053325	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
13	nsv933309	chr22:33825232-34053000	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
14	esv2763261	chr22:33831348-34288389	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
15	nsv588931	chr22:33834668-33907964	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
16	nsv1063275	chr22:33847076-33934464	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	nsv914984	chr22:33848936-33907964	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
18	nsv917167	chr22:33852676-34137036	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
19	esv2751963	chr22:33855512-33935897	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
20	nsv1065776	chr22:33860774-33934464	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
21	nsv1062832	chr22:33861531-34143295	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
22	nsv544686	chr22:33861531-34143295	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
23	nsv1064943	chr22:33862239-33934464	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
24	nsv1063011	chr22:33863218-33934464	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
25	nsv914986	chr22:33863218-33967289	Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
26	nsv1067480	chr22:33865381-33934464	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
27	nsv459877	chr22:33866854-33932624	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
28	nsv588932	chr22:33866854-33932624	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
29	nsv1066694	chr22:33868123-33928973	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
30	nsv544687	chr22:33868123-33928973	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
31	esv2758541	chr22:33868945-33909546	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
32	esv2758832	chr22:33868945-33909546	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
33	nsv1060320	chr22:33875165-33911764	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
34	nsv544688	chr22:33875165-33911764	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1540299	TTC28AS	cis	cerebellum	SCAN
rs1540299	RFPL3	cis	parietal	SCAN
rs1540299	SFI1	cis	parietal	SCAN
rs1540299	GAS2L1	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:33885000-33915200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr22:33889000-33909200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr22:33889200-33915000	Weak transcription	Primary B cells from peripheral blood	blood
4	chr22:33893800-33915000	Weak transcription	GM12878-XiMat	blood
5	chr22:33901200-33909000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr22:33901400-33911800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr22:33901600-33909000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr22:33902400-33909000	Weak transcription	Aorta	Aorta
9	chr22:33902600-33909000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr22:33902600-33909000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr22:33903000-33911200	Weak transcription	Right Ventricle	heart
12	chr22:33903200-33909400	Weak transcription	Brain Angular Gyrus	brain
13	chr22:33904400-33909400	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr22:33904600-33909000	Weak transcription	Fetal Heart	heart
15	chr22:33904800-33909000	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr22:33904800-33915200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr22:33905400-33908600	Weak transcription	Left Ventricle	heart
18	chr22:33905400-33917200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr22:33905600-33908200	Enhancers	HepG2	liver
20	chr22:33906400-33909200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr22:33906400-33935800	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr22:33906600-33909000	Weak transcription	Liver	Liver
23	chr22:33906600-33909200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr22:33906600-33920000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr22:33906800-33911600	Weak transcription	Fetal Intestine Large	intestine
26	chr22:33906800-33911800	Weak transcription	Gastric	stomach
27	chr22:33907000-33909800	Weak transcription	Stomach Mucosa	stomach
28	chr22:33907400-33909200	Weak transcription	Brain Anterior Caudate	brain
29	chr22:33907800-33909000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr22:33907800-33909000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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