Variant report

Variant	rs727892
Chromosome Location	chr22:29443709-29443710
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29442673..29444678-chr22:29547602..29550105,2	K562	blood:
2	chr22:29436460..29439991-chr22:29442261..29446083,4	MCF-7	breast:
3	chr22:29195630..29197790-chr22:29440698..29444304,5	MCF-7	breast:
4	chr22:29432585..29435397-chr22:29443642..29445471,2	K562	blood:
5	chr22:29440576..29442454-chr22:29442829..29445224,2	K562	blood:

Variant related genes	Relation type
ENSG00000226471	Chromatin interaction
ENSG00000100219	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs12484832	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12485244	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17440734	1.00[CEU][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap]
rs1977047	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1983553	0.96[CEU][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2064084	0.96[CEU][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap]
rs2072774	0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs2103544	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2347789	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2347790	0.88[ASW][hapmap];0.92[CEU][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28541979	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4140643	0.92[CEU][hapmap];0.83[GIH][hapmap];0.83[TSI][hapmap]
rs4333023	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4404379	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4594553	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4616575	0.82[AMR][1000 genomes]
rs469994	1.00[CEU][hapmap]
rs4820794	0.92[CEU][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4823002	0.96[CEU][hapmap];0.83[GIH][hapmap];0.85[TSI][hapmap]
rs4823003	0.96[CEU][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap]
rs4823005	0.96[CEU][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs5997430	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5997431	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs5997432	0.82[ASN][1000 genomes]
rs5997433	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs5997434	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5997435	0.91[EUR][1000 genomes]
rs6005955	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6005956	0.92[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6005958	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs6005959	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6005964	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs6005965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6005967	0.88[ASW][hapmap];0.96[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs713834	0.96[CEU][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.86[JPT][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7284304	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7287517	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7290304	0.96[CEU][hapmap];0.81[GIH][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs738246	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8137254	0.92[CEU][hapmap];0.80[GIH][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes]
rs8137499	1.00[CEU][hapmap]
rs8142591	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs874915	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs874916	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs874917	0.82[ASN][1000 genomes]
rs9608719	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs9608721	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9613768	0.83[TSI][hapmap]
rs9613771	0.82[EUR][1000 genomes]
rs9613776	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9613777	0.88[ASW][hapmap];0.92[CEU][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9613782	0.81[CHD][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap]
rs9613784	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9613785	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs964589	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][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	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv531586	chr22:29252132-29902266	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs727892	DDT	cis	cerebellum	SCAN
rs727892	GGT5	cis	parietal	SCAN
rs727892	SEZ6L	cis	cerebellum	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29427400-29448400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr22:29427800-29451400	Weak transcription	Psoas Muscle	Psoas
3	chr22:29429000-29444000	Weak transcription	Right Ventricle	heart
4	chr22:29436800-29443800	Weak transcription	Hela-S3	cervix
5	chr22:29436800-29445600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr22:29437200-29443800	Weak transcription	Fetal Heart	heart
7	chr22:29437200-29450800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr22:29437800-29448800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr22:29437800-29450200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr22:29438000-29447200	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr22:29438200-29447400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr22:29438400-29449800	Strong transcription	Fetal Stomach	stomach
13	chr22:29438400-29451800	Strong transcription	Fetal Intestine Small	intestine
14	chr22:29438600-29445400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr22:29438600-29445600	Strong transcription	Fetal Muscle Trunk	muscle
16	chr22:29439000-29447400	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr22:29439000-29447400	Strong transcription	Fetal Intestine Large	intestine
18	chr22:29439000-29447400	Strong transcription	Stomach Smooth Muscle	stomach
19	chr22:29439000-29449800	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr22:29439000-29450200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr22:29439200-29445400	Strong transcription	Fetal Muscle Leg	muscle
22	chr22:29439200-29447000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr22:29439200-29447400	Strong transcription	H9 Cell Line	embryonic stem cell
24	chr22:29439200-29447400	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr22:29439200-29447400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
26	chr22:29439200-29447400	Strong transcription	Pancreas	Pancrea
27	chr22:29439200-29447600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr22:29439200-29447600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr22:29439400-29447000	Strong transcription	Skeletal Muscle Male	skeletal muscle
30	chr22:29439400-29447400	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr22:29439400-29448400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr22:29439400-29448400	Strong transcription	Brain Anterior Caudate	brain
33	chr22:29439600-29444600	Strong transcription	ES-I3 Cell Line	embryonic stem cell
34	chr22:29439600-29444800	Strong transcription	Left Ventricle	heart
35	chr22:29439600-29445200	Strong transcription	Fetal Kidney	kidney
36	chr22:29440000-29445400	Strong transcription	Fetal Lung	lung
37	chr22:29440000-29446400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr22:29440000-29447400	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr22:29440000-29447400	Strong transcription	Spleen	Spleen
40	chr22:29440000-29447600	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr22:29440000-29451400	Weak transcription	Fetal Thymus	thymus
42	chr22:29440200-29448800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr22:29440400-29447000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr22:29440400-29447400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
45	chr22:29440400-29447400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr22:29440600-29445200	Strong transcription	Placenta	Placenta
47	chr22:29440600-29446400	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr22:29440600-29447400	Strong transcription	Lung	lung
49	chr22:29440800-29443800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr22:29440800-29443800	Weak transcription	Brain Germinal Matrix	brain

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