Variant report

Variant	rs7038258
Chromosome Location	chr9:116260289-116260290
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:116259892..116262727-chr9:116263067..116266319,3	MCF-7	breast:
2	chr9:116260155..116261914-chr9:116342825..116344941,2	MCF-7	breast:
3	chr9:116256606..116259103-chr9:116259265..116261793,2	MCF-7	breast:
4	chr9:116254507..116256265-chr9:116258071..116260770,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138835	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10981835	0.82[YRI][hapmap]
rs12346476	1.00[EUR][1000 genomes]
rs60969910	1.00[EUR][1000 genomes]
rs6478021	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7023224	1.00[EUR][1000 genomes]
rs7027261	1.00[EUR][1000 genomes]
rs7032245	1.00[EUR][1000 genomes]
rs7032414	1.00[EUR][1000 genomes]
rs7033489	1.00[EUR][1000 genomes]
rs7042609	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73538901	1.00[EUR][1000 genomes]
rs73544687	1.00[EUR][1000 genomes]
rs73544688	1.00[EUR][1000 genomes]
rs7851265	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7853612	1.00[EUR][1000 genomes]
rs7856713	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7864169	1.00[EUR][1000 genomes]
rs7865642	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7866866	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7867017	1.00[EUR][1000 genomes]
rs7870008	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv893747	chr9:116214058-116386438	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS 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	13 gene(s)	inside rSNPs	diseases
3	nsv466508	chr9:116244982-116362738	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv615215	chr9:116244982-116362738	Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv526579	chr9:116244982-116391162	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:116227400-116263800	Weak transcription	Colonic Mucosa	Colon
2	chr9:116242000-116263600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:116242000-116266200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr9:116248600-116261600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr9:116248800-116261600	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr9:116251000-116263800	Weak transcription	Esophagus	oesophagus
7	chr9:116251200-116263200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr9:116251600-116283800	Weak transcription	Hela-S3	cervix
9	chr9:116251800-116261600	Weak transcription	HepG2	liver
10	chr9:116252400-116273200	Weak transcription	Pancreas	Pancrea
11	chr9:116252600-116262000	Weak transcription	A549	lung
12	chr9:116255400-116264000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr9:116255400-116264200	Weak transcription	Fetal Kidney	kidney
14	chr9:116255600-116263000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr9:116255600-116265400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr9:116255600-116266600	Weak transcription	Stomach Mucosa	stomach
17	chr9:116255600-116269400	Weak transcription	Colon Smooth Muscle	Colon
18	chr9:116255600-116275800	Weak transcription	Primary hematopoietic stem cells	blood
19	chr9:116255800-116263800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr9:116255800-116263800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr9:116255800-116264800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
22	chr9:116256000-116261800	Weak transcription	Fetal Thymus	thymus
23	chr9:116256000-116261800	Weak transcription	Lung	lung
24	chr9:116256000-116262400	Weak transcription	Right Ventricle	heart
25	chr9:116256000-116264800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr9:116256200-116261600	Weak transcription	Right Atrium	heart
27	chr9:116256600-116261600	Weak transcription	Fetal Heart	heart
28	chr9:116256800-116263800	Strong transcription	Fetal Intestine Small	intestine
29	chr9:116257000-116262400	Weak transcription	Left Ventricle	heart
30	chr9:116257400-116270800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr9:116257800-116262400	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr9:116257800-116263400	Strong transcription	Stomach Smooth Muscle	stomach
33	chr9:116257800-116263600	Weak transcription	Spleen	Spleen
34	chr9:116258600-116263800	Weak transcription	Fetal Intestine Large	intestine
35	chr9:116259000-116262400	Weak transcription	Fetal Muscle Leg	muscle
36	chr9:116259200-116274000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr9:116259200-116274200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr9:116259400-116260800	Strong transcription	Aorta	Aorta
39	chr9:116259600-116261800	Strong transcription	Skeletal Muscle Male	skeletal muscle
40	chr9:116259600-116263800	Strong transcription	Fetal Stomach	stomach
41	chr9:116259800-116263800	Weak transcription	Gastric	stomach
42	chr9:116260200-116260400	Enhancers	Placenta	Placenta
43	chr9:116260200-116262200	Strong transcription	Duodenum Mucosa	Duodenum
44	chr9:116260200-116263600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr9:116260200-116265400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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