Variant report

Variant	rs738246
Chromosome Location	chr22:29439939-29439940
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:29426264..29428504-chr22:29439113..29440872,2	K562	blood:
2	chr22:29195509..29198134-chr22:29437512..29441446,4	K562	blood:
3	chr22:29436800..29439536-chr22:29439547..29442052,2	K562	blood:
4	chr22:29436460..29439991-chr22:29442261..29446083,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000177993	Chromatin interaction
ENSG00000226471	Chromatin interaction
ENSG00000100219	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12484832	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12485244	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17440734	0.96[CEU][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.87[MEX][hapmap]
rs1977047	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1983553	0.92[CEU][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2064084	0.92[CEU][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap]
rs2072774	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2103544	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2347789	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2347790	1.00[ASW][hapmap];0.96[CEU][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.84[LWK][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28541979	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4140643	0.96[CEU][hapmap];0.81[TSI][hapmap]
rs4333023	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4404379	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4594553	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4616575	0.83[AMR][1000 genomes]
rs469994	0.96[CEU][hapmap]
rs4820794	0.96[CEU][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4823002	1.00[CEU][hapmap];0.83[TSI][hapmap]
rs4823003	0.92[CEU][hapmap]
rs4823005	0.92[CEU][hapmap]
rs5997430	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5997431	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5997432	0.80[ASN][1000 genomes]
rs5997433	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs5997434	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5997435	0.90[EUR][1000 genomes]
rs6005955	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6005956	0.96[CEU][hapmap];0.92[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6005958	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs6005959	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6005964	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs6005965	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6005967	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs713834	1.00[CEU][hapmap];0.87[GIH][hapmap];0.82[JPT][hapmap];0.85[TSI][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs727892	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]
rs7284304	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7287517	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7290304	0.92[CEU][hapmap]
rs8137254	0.96[CEU][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes]
rs8137499	0.96[CEU][hapmap]
rs8142591	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs874915	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs874916	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs874917	0.80[ASN][1000 genomes]
rs9608719	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs9608721	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9613768	0.81[TSI][hapmap]
rs9613771	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9613776	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9613777	1.00[ASW][hapmap];0.96[CEU][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.89[LWK][hapmap];0.92[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9613782	0.80[MEX][hapmap];0.81[TSI][hapmap]
rs9613784	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9613785	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs964589	1.00[CEU][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.88[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

No data

Chromatin state (count:100 , 50 per page) page: 1 2

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	chr22:29428000-29441800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr22:29428600-29440400	Weak transcription	Esophagus	oesophagus
5	chr22:29428600-29440800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr22:29428800-29443600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr22:29429000-29440600	Weak transcription	Colonic Mucosa	Colon
8	chr22:29429000-29444000	Weak transcription	Right Ventricle	heart
9	chr22:29433800-29440600	Weak transcription	Lung	lung
10	chr22:29435400-29440000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr22:29435400-29440400	Weak transcription	Gastric	stomach
12	chr22:29436400-29440800	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr22:29436600-29440000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr22:29436800-29441200	Genic enhancers	HepG2	liver
15	chr22:29436800-29442600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr22:29436800-29443800	Weak transcription	Hela-S3	cervix
17	chr22:29436800-29445600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr22:29437200-29440000	Weak transcription	Duodenum Mucosa	Duodenum
19	chr22:29437200-29440000	Weak transcription	Ovary	ovary
20	chr22:29437200-29440000	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr22:29437200-29440400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr22:29437200-29440400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr22:29437200-29440600	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr22:29437200-29440600	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr22:29437200-29441400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr22:29437200-29442200	Weak transcription	Small Intestine	intestine
27	chr22:29437200-29443000	Weak transcription	K562	blood
28	chr22:29437200-29443200	Weak transcription	Brain Angular Gyrus	brain
29	chr22:29437200-29443800	Weak transcription	Fetal Heart	heart
30	chr22:29437200-29450800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr22:29437400-29440000	Weak transcription	Brain Cingulate Gyrus	brain
32	chr22:29437600-29440400	Weak transcription	Fetal Brain Female	brain
33	chr22:29437600-29440800	Weak transcription	Adipose Nuclei	Adipose
34	chr22:29437800-29440000	Weak transcription	Fetal Lung	lung
35	chr22:29437800-29448800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr22:29437800-29450200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr22:29438000-29440000	Weak transcription	Dnd41	blood
38	chr22:29438000-29440600	Weak transcription	Colon Smooth Muscle	Colon
39	chr22:29438000-29442000	Weak transcription	Brain Hippocampus Middle	brain
40	chr22:29438000-29442800	Weak transcription	Fetal Brain Male	brain
41	chr22:29438000-29447200	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr22:29438200-29440000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr22:29438200-29447400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr22:29438400-29449800	Strong transcription	Fetal Stomach	stomach
45	chr22:29438400-29451800	Strong transcription	Fetal Intestine Small	intestine
46	chr22:29438600-29440400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr22:29438600-29440400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr22:29438600-29445400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr22:29438600-29445600	Strong transcription	Fetal Muscle Trunk	muscle
50	chr22:29439000-29441400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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