Variant report

Variant	rs12004054
Chromosome Location	chr9:95842629-95842630
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:95833185..95836026-chr9:95840723..95843661,2	MCF-7	breast:
2	chr9:95824479..95826328-chr9:95840688..95842946,2	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10821066	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10992626	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10992628	0.88[ASN][1000 genomes]
rs1131773	0.90[ASN][1000 genomes]
rs12352182	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12375973	0.90[ASN][1000 genomes]
rs16908779	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28468656	0.92[ASN][1000 genomes]
rs4077811	0.94[ASN][1000 genomes]
rs4078501	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4341217	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4636265	0.87[ASN][1000 genomes]
rs57866297	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61478314	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6479448	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6479450	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7025686	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7046192	0.85[EUR][1000 genomes]
rs7849306	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7870953	0.85[EUR][1000 genomes]
rs9695137	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9696341	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9696357	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526296	chr9:95708192-96030392	Enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1054767	chr9:95738134-95875977	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv1035230	chr9:95770249-95934982	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv893575	chr9:95781040-95854013	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv893576	chr9:95789960-96158277	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers 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	29 gene(s)	inside rSNPs	diseases
6	esv1824329	chr9:95811604-95921347	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv893577	chr9:95812707-95872216	Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv893578	chr9:95818641-95887320	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95824600-95854000	Weak transcription	Gastric	stomach
2	chr9:95828600-95845000	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr9:95833000-95842800	Weak transcription	GM12878-XiMat	blood
4	chr9:95834400-95857400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr9:95834800-95846600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr9:95834800-95848000	Weak transcription	Aorta	Aorta
7	chr9:95835000-95842800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr9:95835400-95843400	Weak transcription	Brain Hippocampus Middle	brain
9	chr9:95835400-95845000	Weak transcription	Lung	lung
10	chr9:95835400-95845400	Weak transcription	Fetal Intestine Large	intestine
11	chr9:95835400-95846400	Weak transcription	Esophagus	oesophagus
12	chr9:95835400-95846600	Weak transcription	Liver	Liver
13	chr9:95835400-95848800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr9:95835400-95849000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr9:95835600-95843400	Weak transcription	Fetal Muscle Leg	muscle
16	chr9:95835600-95848000	Weak transcription	Colonic Mucosa	Colon
17	chr9:95836200-95850000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr9:95836200-95855600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr9:95836400-95845000	Weak transcription	Fetal Stomach	stomach
20	chr9:95837400-95843200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr9:95837800-95844200	Strong transcription	Primary T cells from cord blood	blood
22	chr9:95837800-95845000	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr9:95838000-95844600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr9:95838200-95843600	Strong transcription	Spleen	Spleen
25	chr9:95838200-95843800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr9:95838200-95851000	Strong transcription	Primary B cells from peripheral blood	blood
27	chr9:95838400-95843800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr9:95839200-95843600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
29	chr9:95839200-95843600	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr9:95839400-95843200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr9:95839400-95844800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr9:95839600-95845000	Strong transcription	Thymus	Thymus
33	chr9:95839800-95843800	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr9:95839800-95851000	Weak transcription	K562	blood
35	chr9:95840400-95843400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr9:95840400-95857000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr9:95840600-95845200	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr9:95840800-95845000	Strong transcription	Fetal Thymus	thymus
39	chr9:95841000-95843600	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr9:95841000-95844800	Weak transcription	Primary hematopoietic stem cells	blood
41	chr9:95841200-95849400	Strong transcription	Ovary	ovary
42	chr9:95841400-95844000	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr9:95841400-95844400	Strong transcription	Primary B cells from cord blood	blood
44	chr9:95841600-95844000	Strong transcription	Fetal Intestine Small	intestine
45	chr9:95841600-95844400	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr9:95841800-95843600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr9:95841800-95844000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr9:95842000-95842800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr9:95842200-95843400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr9:95842200-95843600	Weak transcription	Fetal Muscle Trunk	muscle

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