Variant report

Variant	rs9942412
Chromosome Location	chr5:154160451-154160452
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:154158515..154161284-chr5:154235913..154238462,2	K562	blood:
2	chr5:154158451..154160663-chr5:154164358..154166909,3	MCF-7	breast:
3	chr5:154151385..154153346-chr5:154159128..154160723,2	MCF-7	breast:
4	chr5:154132476..154143251-chr5:154145354..154162500,38	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155508	Chromatin interaction
ENSG00000155506	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs12188828	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12300	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17116411	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17116414	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17116421	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17116442	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17116534	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs186971	0.82[ASN][1000 genomes]
rs2112223	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2396999	0.84[EUR][1000 genomes]
rs2544874	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2544875	0.81[EUR][1000 genomes]
rs2544876	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2544880	0.81[EUR][1000 genomes]
rs2560063	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2644744	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2688186	0.81[EUR][1000 genomes]
rs2688187	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2688188	0.81[EUR][1000 genomes]
rs2688189	0.81[EUR][1000 genomes]
rs2688190	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2688191	0.81[EUR][1000 genomes]
rs2688193	0.80[EUR][1000 genomes]
rs2688198	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2688199	0.88[ASN][1000 genomes]
rs2688200	0.81[EUR][1000 genomes]
rs2688201	0.81[EUR][1000 genomes]
rs2688206	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2688208	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs39614	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55770418	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs56374414	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs58415346	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59525998	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59749917	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6884416	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs702742	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73276742	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7723269	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7728194	0.85[EUR][1000 genomes]
rs816717	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs816718	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs816720	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs816722	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs888694	0.84[ASN][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	nsv830521	chr5:154147567-154244266	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv965536	chr5:154155200-154163441	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:154147400-154161800	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr5:154151200-154162200	Weak transcription	Primary hematopoietic stem cells	blood
3	chr5:154151200-154162800	Weak transcription	Primary B cells from cord blood	blood
4	chr5:154151400-154161600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr5:154151600-154161400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr5:154151600-154161800	Weak transcription	Fetal Lung	lung
7	chr5:154151600-154162200	Weak transcription	Fetal Brain Female	brain
8	chr5:154151600-154163000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr5:154151600-154163400	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr5:154151600-154171200	Weak transcription	Fetal Brain Male	brain
11	chr5:154151800-154161800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr5:154152600-154168200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr5:154152600-154168400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr5:154154000-154162000	Weak transcription	Esophagus	oesophagus
15	chr5:154155200-154162200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr5:154155400-154161400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr5:154155400-154161400	Weak transcription	Brain Angular Gyrus	brain
18	chr5:154155800-154160600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr5:154155800-154161800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr5:154156000-154161400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr5:154156000-154161400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr5:154156000-154162200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:154156000-154163400	Weak transcription	Brain Germinal Matrix	brain
24	chr5:154156200-154161600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr5:154156400-154161600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr5:154156400-154162200	Weak transcription	Aorta	Aorta
27	chr5:154156800-154161200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr5:154156800-154161200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr5:154157800-154164200	Enhancers	Liver	Liver
30	chr5:154157800-154168000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr5:154157800-154168200	Enhancers	Primary T cells fromperipheralblood	blood
32	chr5:154157800-154168200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr5:154157800-154168400	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr5:154158000-154160800	Enhancers	Primary T cells from cord blood	blood
35	chr5:154158000-154160800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
36	chr5:154158000-154163800	Enhancers	Duodenum Mucosa	Duodenum
37	chr5:154158000-154164200	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr5:154158000-154168200	Enhancers	Left Ventricle	heart
39	chr5:154158000-154168400	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr5:154158200-154168200	Enhancers	Spleen	Spleen
41	chr5:154158400-154161600	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr5:154158600-154160800	Enhancers	Right Ventricle	heart
43	chr5:154158600-154162200	Enhancers	Primary B cells from peripheral blood	blood
44	chr5:154158800-154160600	Weak transcription	Small Intestine	intestine
45	chr5:154158800-154160800	Enhancers	Lung	lung
46	chr5:154158800-154161400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr5:154158800-154161600	Weak transcription	Brain Substantia Nigra	brain
48	chr5:154158800-154168200	Enhancers	Pancreas	Pancrea
49	chr5:154159000-154160600	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr5:154159000-154161400	Weak transcription	HUES48 Cell Line	embryonic stem cell

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