Variant report

Variant	rs7042492
Chromosome Location	chr9:96042924-96042925
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:95945010..95947116-chr9:96042384..96044882,2	MCF-7	breast:
2	chr9:95895313..95896852-chr9:96041035..96043000,2	MCF-7	breast:
3	chr9:96040692..96043610-chr9:96075654..96077486,2	K562	blood:

Variant related genes	Relation type
ENSG00000131669	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10119816	0.84[AMR][1000 genomes]
rs10733747	1.00[EUR][1000 genomes]
rs10761206	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10761208	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10821104	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1111776	0.96[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12683662	0.92[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12684392	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12684553	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1343631	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1889338	0.92[YRI][hapmap]
rs1891970	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1931365	0.97[EUR][1000 genomes]
rs1931366	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1931367	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1931368	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1936401	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2151714	0.92[YRI][hapmap]
rs2169756	0.92[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2991376	1.00[YRI][hapmap]
rs2995999	1.00[YRI][hapmap]
rs3001449	0.82[AFR][1000 genomes]
rs3847306	1.00[CEU][hapmap]
rs4147136	0.97[EUR][1000 genomes]
rs4548243	0.92[YRI][hapmap]
rs4743908	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4743909	0.97[EUR][1000 genomes]
rs4743913	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs4743914	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs4744209	0.97[EUR][1000 genomes]
rs4744210	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4744214	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56161352	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs56311541	0.84[AMR][1000 genomes]
rs58228786	0.84[AMR][1000 genomes]
rs58965550	0.84[AMR][1000 genomes]
rs6479470	0.97[EUR][1000 genomes]
rs6479472	0.97[EUR][1000 genomes]
rs6479473	1.00[CEU][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7020940	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7021187	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7025514	1.00[CEU][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7025611	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs7031917	1.00[CEU][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes]
rs7035727	0.84[AMR][1000 genomes]
rs7042028	0.94[EUR][1000 genomes]
rs7044229	0.87[AFR][1000 genomes]
rs73651379	0.84[AMR][1000 genomes]
rs73651384	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs7853075	0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs7856268	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7866298	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7872608	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9657693	0.92[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv893580	chr9:95855100-96099377	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv430082	chr9:95905745-96095045	Genic enhancers Enhancers Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv893582	chr9:95963114-96116937	Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv893583	chr9:95996573-96091688	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv893584	chr9:96002983-96116937	Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96006200-96043800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:96027200-96051200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr9:96027200-96056000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr9:96027200-96061000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr9:96031400-96054600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr9:96031400-96055000	Weak transcription	Colonic Mucosa	Colon
7	chr9:96031400-96062800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr9:96032600-96043400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr9:96033000-96054600	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr9:96033000-96055000	Weak transcription	Brain Anterior Caudate	brain
11	chr9:96033000-96067200	Weak transcription	Brain Angular Gyrus	brain
12	chr9:96033400-96062800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr9:96033400-96067000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr9:96033400-96077200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr9:96033600-96044400	Weak transcription	Left Ventricle	heart
16	chr9:96033600-96046000	Weak transcription	Pancreas	Pancrea
17	chr9:96033600-96050200	Weak transcription	Fetal Intestine Small	intestine
18	chr9:96033600-96054600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr9:96033600-96060200	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr9:96033600-96061000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr9:96033600-96072800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr9:96033800-96054600	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr9:96033800-96060400	Weak transcription	Colon Smooth Muscle	Colon
24	chr9:96035800-96051600	Weak transcription	Fetal Intestine Large	intestine
25	chr9:96040600-96049600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr9:96041000-96049400	Weak transcription	Brain Germinal Matrix	brain
27	chr9:96041000-96050400	Weak transcription	HepG2	liver
28	chr9:96041000-96052400	Weak transcription	Stomach Smooth Muscle	stomach
29	chr9:96041400-96046200	Weak transcription	Fetal Brain Female	brain
30	chr9:96041400-96052000	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr9:96041600-96044600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr9:96041600-96056800	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr9:96041800-96054600	Weak transcription	Duodenum Mucosa	Duodenum
34	chr9:96042600-96044200	Enhancers	HMEC	breast
35	chr9:96042600-96044400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr9:96042800-96043600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr9:96042800-96043800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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