Variant report

Variant	rs9472159
Chromosome Location	chr6:43919695-43919696
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:23)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:23 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:43918731..43921612-chr6:43946723..43948842,2	K562	blood:
2	chr6:43735432..43742006-chr6:43916130..43924754,17	K562	blood:
3	chr6:43777358..43779209-chr6:43919551..43921782,2	MCF-7	breast:
4	chr6:43751843..43754586-chr6:43919139..43921023,2	K562	blood:
5	chr6:43736949..43737612-chr6:43919103..43919705,2	MCF-7	breast:
6	chr6:43784672..43785538-chr6:43918690..43919959,3	MCF-7	breast:
7	chr6:43769556..43771806-chr6:43919110..43920612,2	MCF-7	breast:
8	chr6:43734091..43739914-chr6:43917004..43923314,11	MCF-7	breast:
9	chr6:43738015..43740761-chr6:43916683..43921119,5	MCF-7	breast:
10	chr6:43919484..43919988-chr6:44077760..44078281,2	MCF-7	breast:
11	chr6:43917227..43922653-chr6:44039743..44042402,5	K562	blood:
12	chr6:43772078..43772580-chr6:43919115..43920015,2	MCF-7	breast:
13	chr6:43918507..43921247-chr6:44026207..44027976,2	K562	blood:
14	chr6:43918927..43920451-chr6:43969852..43972429,2	MCF-7	breast:
15	chr6:43894781..43895757-chr6:43918790..43919707,5	MCF-7	breast:
16	chr6:43919296..43919870-chr6:43936871..43937698,2	MCF-7	breast:
17	chr6:43919002..43920079-chr6:44042087..44042920,3	K562	blood:
18	chr6:43918917..43921622-chr6:44030358..44031978,2	MCF-7	breast:
19	chr6:43919558..43922276-chr6:43963136..43965900,2	MCF-7	breast:
20	chr6:43919091..43920008-chr6:43968758..43969373,2	MCF-7	breast:
21	chr6:43772118..43772900-chr6:43919246..43920025,3	MCF-7	breast:
22	chr6:43735367..43746902-chr6:43913394..43925044,24	K562	blood:
23	chr6:43664559..43666179-chr6:43919165..43920704,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000112715	Chromatin interaction
ENSG00000231881	Chromatin interaction
ENSG00000237686	Chromatin interaction
ENSG00000272114	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11757868	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11757888	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11757903	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12205248	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13206436	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4320361	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4349808	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4349809	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4413611	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4513773	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4637627	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6921438	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7763440	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7767396	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9369434	0.88[JPT][hapmap]
rs9472168	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9472172	0.84[EUR][1000 genomes];0.81[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	nsv931987	chr6:43624625-44350167	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	201 gene(s)	inside rSNPs	diseases
2	nsv428480	chr6:43764313-43929172	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9472159	SRF	cis	parietal	SCAN
rs9472159	MED20	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:43909200-43922200	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr6:43916600-43920000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:43916600-43920200	Enhancers	Fetal Lung	lung
4	chr6:43916600-43921600	Enhancers	K562	blood
5	chr6:43917000-43921800	Weak transcription	Left Ventricle	heart
6	chr6:43917000-43921800	Weak transcription	Psoas Muscle	Psoas
7	chr6:43918200-43919800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr6:43918400-43919800	Enhancers	Liver	Liver
9	chr6:43918400-43920000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr6:43918600-43920400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr6:43918600-43920400	Enhancers	Fetal Intestine Small	intestine
12	chr6:43918600-43921200	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr6:43918600-43923200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr6:43918800-43919800	Enhancers	Right Atrium	heart
15	chr6:43918800-43919800	Flanking Bivalent TSS/Enh	HepG2	liver
16	chr6:43918800-43920000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr6:43918800-43920000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr6:43918800-43920000	Enhancers	Right Ventricle	heart
19	chr6:43918800-43920200	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr6:43918800-43920400	Enhancers	Fetal Heart	heart
21	chr6:43918800-43920400	Enhancers	Fetal Intestine Large	intestine
22	chr6:43918800-43923400	Enhancers	Fetal Muscle Leg	muscle
23	chr6:43919000-43920000	Enhancers	Lung	lung
24	chr6:43919000-43920000	Enhancers	Placenta Amnion	Placenta Amnion
25	chr6:43919000-43920200	Enhancers	Fetal Stomach	stomach
26	chr6:43919000-43921400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr6:43919200-43920000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr6:43919200-43920400	Enhancers	Fetal Thymus	thymus
29	chr6:43919200-43921200	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr6:43919200-43921600	Weak transcription	Spleen	Spleen
31	chr6:43919400-43919800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr6:43919400-43920000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr6:43919400-43920000	Enhancers	Cortex derived primary cultured neurospheres	brain
34	chr6:43919400-43920400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr6:43919400-43920400	Enhancers	Hela-S3	cervix
36	chr6:43919400-43921600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr6:43919400-43922000	Enhancers	Fetal Muscle Trunk	muscle
38	chr6:43919600-43921200	Weak transcription	Pancreas	Pancrea

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