Variant report

Variant	rs28589289
Chromosome Location	chr7:6168100-6168101
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:6160832..6162553-chr7:6165906..6168472,2	K562	blood:
2	chr7:6166316..6168843-chr7:6171200..6174042,2	K562	blood:
3	chr7:6165378..6168843-chr7:6171200..6175503,4	K562	blood:
4	chr7:6160740..6163677-chr7:6167331..6169023,2	K562	blood:

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10046499	0.94[ASN][1000 genomes]
rs10216107	0.94[ASN][1000 genomes]
rs10225119	0.94[ASN][1000 genomes]
rs10226743	0.89[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10228389	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10228430	0.94[ASN][1000 genomes]
rs10242394	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10246266	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10250285	0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10254689	0.83[ASN][1000 genomes]
rs10255598	0.94[ASN][1000 genomes]
rs10255914	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10255918	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10257181	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10257248	0.94[ASN][1000 genomes]
rs10257654	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10257971	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10261466	0.84[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10275021	0.94[ASN][1000 genomes]
rs10279137	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10280585	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10282278	0.94[ASN][1000 genomes]
rs11768047	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs11770730	0.94[ASN][1000 genomes]
rs12667323	0.86[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12667392	0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs13437890	0.94[ASN][1000 genomes]
rs17136048	0.94[ASN][1000 genomes]
rs28385378	1.00[ASN][1000 genomes]
rs28575447	0.89[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs28758696	0.89[AFR][1000 genomes]
rs28880007	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs34123833	0.88[ASN][1000 genomes]
rs56974330	0.80[ASN][1000 genomes]
rs60892137	1.00[ASN][1000 genomes]
rs61750868	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs61753115	1.00[ASN][1000 genomes]
rs61753118	0.88[ASN][1000 genomes]
rs6944071	0.94[ASN][1000 genomes]
rs6949823	0.94[ASN][1000 genomes]
rs7796322	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9655493	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533108	chr7:5488018-6316581	Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	390 gene(s)	inside rSNPs	diseases
2	nsv1033556	chr7:5565080-6186815	Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
3	nsv538710	chr7:5565080-6186815	Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
4	nsv1021989	chr7:5629728-6186815	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
5	nsv948912	chr7:5803903-6623553	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
6	nsv1034060	chr7:5814823-6745710	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
7	nsv538711	chr7:5814823-6745710	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	138 gene(s)	inside rSNPs	diseases
8	nsv1028242	chr7:5819084-6645024	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
9	nsv538712	chr7:5819084-6645024	Weak transcription Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	127 gene(s)	inside rSNPs	diseases
10	nsv949531	chr7:5949371-6753694	Strong transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	129 gene(s)	inside rSNPs	diseases
11	nsv1021037	chr7:6070792-6426966	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
12	nsv538713	chr7:6070792-6426966	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28589289	PSCD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:6145600-6186000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr7:6145600-6186400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr7:6146800-6218200	Weak transcription	Stomach Mucosa	stomach
4	chr7:6150600-6171400	Strong transcription	Dnd41	blood
5	chr7:6157400-6179000	Weak transcription	Fetal Brain Male	brain
6	chr7:6157400-6188400	Weak transcription	Psoas Muscle	Psoas
7	chr7:6157400-6189400	Weak transcription	Fetal Heart	heart
8	chr7:6159000-6168200	Weak transcription	NHLF	lung
9	chr7:6159600-6178200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr7:6159800-6168400	Weak transcription	Small Intestine	intestine
11	chr7:6160600-6201800	Strong transcription	Fetal Thymus	thymus
12	chr7:6161000-6172000	Strong transcription	Primary T cells from cord blood	blood
13	chr7:6161200-6173200	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr7:6161400-6169800	Weak transcription	HSMMtube	muscle
15	chr7:6161400-6171600	Strong transcription	Primary B cells from peripheral blood	blood
16	chr7:6161400-6172000	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr7:6161400-6172200	Strong transcription	Duodenum Mucosa	Duodenum
18	chr7:6161400-6178200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr7:6161400-6180200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr7:6161400-6183800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr7:6161400-6199600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr7:6161400-6202200	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr7:6161600-6168400	Weak transcription	Esophagus	oesophagus
24	chr7:6161600-6169800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr7:6161600-6179200	Weak transcription	Right Ventricle	heart
26	chr7:6161600-6185200	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr7:6161600-6192000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr7:6161800-6168200	Weak transcription	NHDF-Ad	bronchial
29	chr7:6161800-6183800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr7:6162000-6168200	Weak transcription	Hela-S3	cervix
31	chr7:6162000-6169400	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr7:6162000-6176800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr7:6162000-6178400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr7:6162000-6178400	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr7:6162000-6179000	Weak transcription	Colon Smooth Muscle	Colon
36	chr7:6162000-6179400	Weak transcription	HMEC	breast
37	chr7:6162600-6171800	Weak transcription	Fetal Kidney	kidney
38	chr7:6162800-6169800	Weak transcription	Colonic Mucosa	Colon
39	chr7:6162800-6169800	Weak transcription	Gastric	stomach
40	chr7:6162800-6169800	Weak transcription	Pancreas	Pancrea
41	chr7:6162800-6179000	Weak transcription	Brain Hippocampus Middle	brain
42	chr7:6163000-6169600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr7:6163000-6172000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr7:6163000-6175600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr7:6163000-6185000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr7:6163600-6168200	Weak transcription	Osteobl	bone
47	chr7:6163800-6169600	Weak transcription	Brain Angular Gyrus	brain
48	chr7:6164000-6169600	Weak transcription	NHEK	skin
49	chr7:6164000-6169800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr7:6164000-6170400	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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