Variant report

Variant	rs7042943
Chromosome Location	chr9:96078870-96078871
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:96072987..96083429-chr9:96209751..96218385,15	MCF-7	breast:
2	chr9:96077920..96081969-chr9:96088164..96091770,4	MCF-7	breast:

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

Variant related genes	Relation type
ENSG00000048828	Chromatin interaction
ENSG00000188938	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10992646	1.00[ASN][1000 genomes]
rs10992647	1.00[ASN][1000 genomes]
rs10992649	1.00[ASN][1000 genomes]
rs10992650	1.00[ASN][1000 genomes]
rs10992651	1.00[ASN][1000 genomes]
rs10992654	1.00[ASN][1000 genomes]
rs10992656	1.00[ASN][1000 genomes]
rs10992657	1.00[ASN][1000 genomes]
rs10992661	1.00[ASN][1000 genomes]
rs10992681	1.00[MEX][hapmap];0.92[TSI][hapmap]
rs10992699	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992715	0.87[CEU][hapmap]
rs11787888	1.00[MEX][hapmap];0.96[TSI][hapmap]
rs11789723	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12000967	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12002458	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12005950	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12006039	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12550993	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs12554984	0.82[EUR][1000 genomes]
rs13283550	0.85[CEU][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13289160	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13290796	0.85[MEX][hapmap];0.92[TSI][hapmap]
rs13296817	0.87[CEU][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes]
rs13298340	0.86[EUR][1000 genomes]
rs16909074	0.83[EUR][1000 genomes]
rs1931364	1.00[ASN][1000 genomes]
rs2254351	0.87[CEU][hapmap]
rs34187850	0.82[EUR][1000 genomes]
rs34360996	0.83[EUR][1000 genomes]
rs34406556	0.82[EUR][1000 genomes]
rs34590502	0.83[EUR][1000 genomes]
rs35199621	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35383386	0.83[EUR][1000 genomes]
rs35566702	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35807838	0.82[EUR][1000 genomes]
rs36081907	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4743925	0.87[CEU][hapmap]
rs4743926	0.87[CEU][hapmap]
rs4744213	0.85[MEX][hapmap];1.00[ASN][1000 genomes]
rs4744244	0.87[CEU][hapmap]
rs55981123	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58361139	0.82[EUR][1000 genomes]
rs62572859	0.85[EUR][1000 genomes]
rs6479471	0.85[CEU][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479474	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479489	0.87[CEU][hapmap]
rs6479490	0.87[CEU][hapmap]
rs6479491	0.86[CEU][hapmap]
rs7022051	0.85[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs7023262	1.00[ASN][1000 genomes]
rs7032614	0.85[CEU][hapmap]
rs7046002	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs7848843	0.85[CEU][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7857220	0.85[CEU][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7866300	1.00[ASN][1000 genomes]
rs7867954	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7870747	0.82[EUR][1000 genomes]
rs7873162	0.85[MEX][hapmap];0.92[TSI][hapmap]
rs7874101	0.85[MEX][hapmap];0.92[TSI][hapmap]
rs7875384	0.85[MEX][hapmap];1.00[ASN][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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7042943	FCER2	trans	lymphoblastoid	seeQTL

Chromatin state (count:47 , 50 per page) page: 1

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	chr9:96061600-96079000	Weak transcription	Gastric	stomach
4	chr9:96063800-96088600	Weak transcription	Right Atrium	heart
5	chr9:96065000-96079200	Weak transcription	Colonic Mucosa	Colon
6	chr9:96065200-96080000	Weak transcription	Spleen	Spleen
7	chr9:96066000-96082800	Weak transcription	Fetal Thymus	thymus
8	chr9:96067200-96081200	Weak transcription	Fetal Heart	heart
9	chr9:96067600-96079200	Weak transcription	Right Ventricle	heart
10	chr9:96067600-96086800	Weak transcription	Fetal Brain Male	brain
11	chr9:96067800-96086800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr9:96068200-96086200	Weak transcription	Brain Anterior Caudate	brain
13	chr9:96068400-96082400	Weak transcription	Brain Angular Gyrus	brain
14	chr9:96068400-96100400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr9:96068600-96079200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr9:96068600-96080200	Weak transcription	Left Ventricle	heart
17	chr9:96068800-96080800	Weak transcription	Psoas Muscle	Psoas
18	chr9:96068800-96082600	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr9:96069200-96079400	Weak transcription	Fetal Muscle Leg	muscle
20	chr9:96069400-96079600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr9:96069400-96080000	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr9:96070600-96087800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr9:96071400-96079000	Weak transcription	Fetal Stomach	stomach
24	chr9:96072600-96079000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr9:96074000-96088600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr9:96075200-96079200	Weak transcription	Pancreas	Pancrea
27	chr9:96075200-96081000	Weak transcription	Placenta	Placenta
28	chr9:96075400-96079000	Weak transcription	Fetal Intestine Large	intestine
29	chr9:96075400-96079400	Weak transcription	Rectal Smooth Muscle	rectum
30	chr9:96075400-96080400	Weak transcription	Colon Smooth Muscle	Colon
31	chr9:96076200-96088400	Weak transcription	A549	lung
32	chr9:96077000-96083800	Strong transcription	Duodenum Mucosa	Duodenum
33	chr9:96077000-96085200	Strong transcription	Fetal Brain Female	brain
34	chr9:96077200-96081400	Strong transcription	Stomach Smooth Muscle	stomach
35	chr9:96077800-96079000	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr9:96077800-96079000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr9:96077800-96079000	Weak transcription	Fetal Intestine Small	intestine
38	chr9:96078200-96079600	Enhancers	Stomach Mucosa	stomach
39	chr9:96078200-96079800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr9:96078400-96079200	Enhancers	Fetal Lung	lung
41	chr9:96078800-96079600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
42	chr9:96078800-96080000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
43	chr9:96078800-96080200	Weak transcription	HepG2	liver
44	chr9:96078800-96081000	Strong transcription	Brain Germinal Matrix	brain
45	chr9:96078800-96081000	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr9:96078800-96081200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
47	chr9:96078800-96081600	Strong transcription	Rectal Mucosa Donor 31	rectum

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