Variant report

Variant	rs5762400
Chromosome Location	chr22:28308995-28308996
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:28305823..28310839-chr22:28313322..28318569,8	MCF-7	breast:
2	chr22:28295306..28297742-chr22:28307525..28310849,3	MCF-7	breast:
3	chr22:28308235..28310167-chr22:28310580..28312213,2	MCF-7	breast:
4	chr22:28301560..28304524-chr22:28307675..28309326,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000180957	Chromatin interaction
ENSG00000264073	Chromatin interaction
ENSG00000235954	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12160891	0.94[AFR][1000 genomes]
rs2143180	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2267125	0.94[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2345019	0.91[ASN][1000 genomes]
rs28372773	0.87[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs5752670	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs5762398	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs5762404	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs5762410	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs5762412	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs5762425	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs5762428	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs6005672	0.85[AFR][1000 genomes]
rs6005674	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs714743	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs73166732	0.94[AFR][1000 genomes];0.84[AMR][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	nsv1062877	chr22:28163507-28866350	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv588878	chr22:28248840-28314113	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:28247000-28311800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr22:28283600-28310000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr22:28286000-28309000	Weak transcription	Stomach Mucosa	stomach
4	chr22:28286200-28311400	Weak transcription	Right Atrium	heart
5	chr22:28288600-28309400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr22:28289000-28312600	Weak transcription	Psoas Muscle	Psoas
7	chr22:28292800-28309200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr22:28293200-28309000	Weak transcription	Rectal Smooth Muscle	rectum
9	chr22:28293800-28309200	Weak transcription	Brain Substantia Nigra	brain
10	chr22:28293800-28309600	Weak transcription	Right Ventricle	heart
11	chr22:28293800-28311800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr22:28294000-28309200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr22:28295200-28309200	Weak transcription	Brain Angular Gyrus	brain
14	chr22:28295200-28313800	Weak transcription	Colonic Mucosa	Colon
15	chr22:28298400-28314000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr22:28299200-28314000	Weak transcription	Spleen	Spleen
17	chr22:28299400-28310200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
18	chr22:28300400-28309200	Weak transcription	Small Intestine	intestine
19	chr22:28300400-28311400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr22:28300800-28309200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr22:28301400-28309800	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr22:28303800-28311600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr22:28303800-28313000	Weak transcription	Fetal Brain Female	brain
24	chr22:28303800-28313200	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr22:28304000-28309000	Weak transcription	Stomach Smooth Muscle	stomach
26	chr22:28304000-28309200	Weak transcription	Fetal Kidney	kidney
27	chr22:28304000-28309200	Weak transcription	Ovary	ovary
28	chr22:28304000-28309400	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr22:28304000-28313200	Weak transcription	Brain Cingulate Gyrus	brain
30	chr22:28304200-28313000	Weak transcription	Fetal Brain Male	brain
31	chr22:28306200-28309200	Weak transcription	Pancreas	Pancrea
32	chr22:28306200-28310200	Strong transcription	NHEK	skin
33	chr22:28306400-28309400	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr22:28306400-28309400	Weak transcription	Thymus	Thymus
35	chr22:28306400-28309600	Weak transcription	Gastric	stomach
36	chr22:28306400-28313800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr22:28306400-28313800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr22:28306400-28314200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr22:28306400-28314400	Weak transcription	Esophagus	oesophagus
40	chr22:28306600-28309000	Weak transcription	Brain Hippocampus Middle	brain
41	chr22:28306600-28313800	Weak transcription	Lung	lung
42	chr22:28306800-28309400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr22:28306800-28309600	Enhancers	Fetal Heart	heart
44	chr22:28307000-28309000	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr22:28307000-28309000	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr22:28307000-28309200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr22:28307000-28309200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr22:28307000-28309200	Weak transcription	Rectal Mucosa Donor 31	rectum
49	chr22:28307000-28309200	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr22:28307000-28309200	Weak transcription	A549	lung

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