Variant report

Variant	rs4743913
Chromosome Location	chr9:96079462-96079463
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:96072987..96083429-chr9:96209751..96218385,15	MCF-7	breast:
2	chr9:96077920..96081969-chr9:96088164..96091770,4	MCF-7	breast:
3	chr9:96079198..96081765-chr9:96083546..96088659,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM120A-4	chr9:96077770-96079913	NONHSAT133246

Variant related genes	Relation type
ENSG00000188938	Chromatin interaction
ENSG00000048828	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10739946	0.86[EUR][1000 genomes]
rs10761208	1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs1111776	0.96[YRI][hapmap];0.92[AFR][1000 genomes]
rs12683662	0.90[AFR][1000 genomes]
rs12684392	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs1889338	1.00[CEU][hapmap];0.92[YRI][hapmap]
rs1891970	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs2151714	1.00[CEU][hapmap];0.92[YRI][hapmap]
rs2169756	0.92[YRI][hapmap];0.90[AFR][1000 genomes]
rs2494781	0.86[EUR][1000 genomes]
rs28421070	0.90[EUR][1000 genomes]
rs2991376	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs2991380	0.86[EUR][1000 genomes]
rs2991383	0.90[EUR][1000 genomes]
rs2995993	0.90[EUR][1000 genomes]
rs2995994	0.86[EUR][1000 genomes]
rs2995999	1.00[CEU][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs3001449	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3001453	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4548243	1.00[CEU][hapmap];0.92[YRI][hapmap]
rs4743914	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4744214	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs56161352	0.89[AFR][1000 genomes]
rs6479473	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs7020195	1.00[CEU][hapmap]
rs7025514	0.92[YRI][hapmap];0.85[AFR][1000 genomes]
rs7025611	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7027660	0.81[EUR][1000 genomes]
rs7031917	0.94[YRI][hapmap];0.85[AFR][1000 genomes]
rs7042492	1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs7044229	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs73651384	0.85[AFR][1000 genomes]
rs7853075	0.92[YRI][hapmap];0.89[AFR][1000 genomes]
rs7866298	1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs7872608	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs999326	1.00[CEU][hapmap]

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:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:96055600-96080200	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr9:96056400-96079800	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr9:96063800-96088600	Weak transcription	Right Atrium	heart
4	chr9:96065200-96080000	Weak transcription	Spleen	Spleen
5	chr9:96066000-96082800	Weak transcription	Fetal Thymus	thymus
6	chr9:96067200-96081200	Weak transcription	Fetal Heart	heart
7	chr9:96067600-96086800	Weak transcription	Fetal Brain Male	brain
8	chr9:96067800-96086800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr9:96068200-96086200	Weak transcription	Brain Anterior Caudate	brain
10	chr9:96068400-96082400	Weak transcription	Brain Angular Gyrus	brain
11	chr9:96068400-96100400	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr9:96068600-96080200	Weak transcription	Left Ventricle	heart
13	chr9:96068800-96080800	Weak transcription	Psoas Muscle	Psoas
14	chr9:96068800-96082600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr9:96069400-96079600	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr9:96069400-96080000	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr9:96070600-96087800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr9:96074000-96088600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr9:96075200-96081000	Weak transcription	Placenta	Placenta
20	chr9:96075400-96080400	Weak transcription	Colon Smooth Muscle	Colon
21	chr9:96076200-96088400	Weak transcription	A549	lung
22	chr9:96077000-96083800	Strong transcription	Duodenum Mucosa	Duodenum
23	chr9:96077000-96085200	Strong transcription	Fetal Brain Female	brain
24	chr9:96077200-96081400	Strong transcription	Stomach Smooth Muscle	stomach
25	chr9:96078200-96079600	Enhancers	Stomach Mucosa	stomach
26	chr9:96078200-96079800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr9:96078800-96079600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
28	chr9:96078800-96080000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
29	chr9:96078800-96080200	Weak transcription	HepG2	liver
30	chr9:96078800-96081000	Strong transcription	Brain Germinal Matrix	brain
31	chr9:96078800-96081000	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr9:96078800-96081200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
33	chr9:96078800-96081600	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr9:96079000-96079600	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
35	chr9:96079000-96079800	Strong transcription	Fetal Stomach	stomach
36	chr9:96079000-96080400	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
37	chr9:96079000-96080400	Strong transcription	Gastric	stomach
38	chr9:96079000-96081000	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
39	chr9:96079000-96081800	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr9:96079000-96082600	Strong transcription	Fetal Intestine Large	intestine
41	chr9:96079000-96083800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr9:96079000-96084600	Strong transcription	Fetal Intestine Small	intestine
43	chr9:96079200-96080200	Strong transcription	Colonic Mucosa	Colon
44	chr9:96079200-96080800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
45	chr9:96079200-96080800	Strong transcription	Right Ventricle	heart
46	chr9:96079200-96081000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr9:96079200-96081000	Strong transcription	Pancreas	Pancrea
48	chr9:96079200-96082000	Weak transcription	Fetal Lung	lung
49	chr9:96079200-96088600	Weak transcription	HUES64 Cell Line	embryonic stem cell
50	chr9:96079400-96079800	Strong transcription	Rectal Smooth Muscle	rectum

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