Variant report

Variant	rs2258889
Chromosome Location	chr9:136652465-136652466
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:136649765..136654574-chr9:136658647..136663860,5	MCF-7	breast:
2	chr9:136645262..136664386-chr9:136851810..136861142,57	MCF-7	breast:
3	chr9:136649018..136654096-chr9:136736895..136740406,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160293	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10119331	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10761399	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10821524	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10821525	0.81[ASN][1000 genomes]
rs10993802	0.91[ASN][1000 genomes]
rs13283160	0.91[ASN][1000 genomes]
rs13292058	0.97[ASN][1000 genomes]
rs1468127	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2023664	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2023665	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2072059	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2073910	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2106373	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2239912	0.84[ASN][1000 genomes]
rs2488561	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2510239	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3824558	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3824560	0.91[ASN][1000 genomes]
rs3824561	0.91[ASN][1000 genomes]
rs7027503	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7032391	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7032952	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7039067	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894081	chr9:136227260-136678954	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv894086	chr9:136281753-136657960	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv870051	chr9:136459745-136656889	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv894114	chr9:136538798-136779153	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv428546	chr9:136541745-136720872	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv831745	chr9:136593702-136780273	Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv894117	chr9:136600201-136716399	Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv831746	chr9:136607829-136750740	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv466622	chr9:136617292-136658816	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv615691	chr9:136617292-136658816	Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv894118	chr9:136624542-136678954	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv894119	chr9:136629399-136657960	Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	nsv894120	chr9:136629399-136662638	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv894121	chr9:136629399-136692787	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	nsv894122	chr9:136632662-136760639	Enhancers Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
16	esv3424363	chr9:136649131-136653429	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	esv3373731	chr9:136650181-136652979	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:136624800-136657800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:136633200-136653400	Strong transcription	HUES6 Cell Line	embryonic stem cell
3	chr9:136633200-136653600	Weak transcription	Brain Angular Gyrus	brain
4	chr9:136636800-136653800	Strong transcription	NHEK	skin
5	chr9:136637400-136653600	Strong transcription	Liver	Liver
6	chr9:136637800-136653200	Weak transcription	Small Intestine	intestine
7	chr9:136639200-136653000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr9:136639400-136653000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr9:136640000-136652600	Weak transcription	Stomach Mucosa	stomach
10	chr9:136640000-136658000	Weak transcription	Fetal Thymus	thymus
11	chr9:136640000-136679400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr9:136640200-136653000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr9:136640200-136658000	Weak transcription	Colon Smooth Muscle	Colon
14	chr9:136640200-136659400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr9:136640400-136652600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr9:136640400-136653000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr9:136640400-136682600	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr9:136640800-136667000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr9:136641600-136654200	Weak transcription	Right Ventricle	heart
20	chr9:136643000-136658000	Weak transcription	Left Ventricle	heart
21	chr9:136643200-136689800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr9:136643400-136653000	Weak transcription	HUVEC	blood vessel
23	chr9:136643800-136672600	Weak transcription	Aorta	Aorta
24	chr9:136644600-136654600	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr9:136644800-136658000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr9:136645000-136664200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr9:136645200-136653200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr9:136645200-136656600	Weak transcription	NHDF-Ad	bronchial
29	chr9:136645200-136658000	Strong transcription	Fetal Stomach	stomach
30	chr9:136645600-136653400	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr9:136646600-136658000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr9:136647200-136654400	Enhancers	Primary B cells from cord blood	blood
33	chr9:136647400-136654800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr9:136647600-136652600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr9:136647800-136657600	Strong transcription	Osteobl	bone
36	chr9:136648000-136657600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr9:136648400-136653400	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr9:136648600-136658200	Weak transcription	Fetal Heart	heart
39	chr9:136649000-136656600	Strong transcription	Placenta Amnion	Placenta Amnion
40	chr9:136649000-136657600	Strong transcription	Brain Germinal Matrix	brain
41	chr9:136650000-136679400	Weak transcription	Right Atrium	heart
42	chr9:136650400-136654000	Weak transcription	Hela-S3	cervix
43	chr9:136650600-136653200	Enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr9:136650600-136653200	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
45	chr9:136650600-136688800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr9:136650800-136653200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
47	chr9:136651200-136652600	Genic enhancers	Duodenum Mucosa	Duodenum
48	chr9:136651200-136652600	Weak transcription	HSMMtube	muscle
49	chr9:136651200-136652800	Flanking Active TSS	GM12878-XiMat	blood
50	chr9:136651200-136656000	Genic enhancers	Fetal Muscle Trunk	muscle

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