Variant report

Variant	rs9609254
Chromosome Location	chr22:31705942-31705943
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:31684965..31688899-chr22:31705650..31709359,6	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LIMK2-2	chr22:31705176-31706049	NONHSAT084875

Variant related genes	Relation type
ENSG00000228839	Chromatin interaction
ENSG00000100100	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1034588	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12152166	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13054220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs131205	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1858821	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2040533	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2073857	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2078803	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2106294	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2228619	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2283879	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2283881	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2413034	0.80[EUR][1000 genomes]
rs2413035	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2413046	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2413047	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2413049	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2899164	0.85[EUR][1000 genomes]
rs34545960	0.83[EUR][1000 genomes]
rs4141404	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4299418	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4603880	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4820042	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4820043	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4820951	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4820962	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4820963	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5749229	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5749243	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5749265	0.84[EUR][1000 genomes]
rs5749267	0.83[EUR][1000 genomes]
rs5749268	0.83[EUR][1000 genomes]
rs5749270	0.83[EUR][1000 genomes]
rs5753521	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5753543	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5753597	0.84[EUR][1000 genomes]
rs5753601	0.84[EUR][1000 genomes]
rs5753610	0.83[EUR][1000 genomes]
rs5753612	0.82[EUR][1000 genomes]
rs5753613	0.82[EUR][1000 genomes]
rs5994394	0.82[EUR][1000 genomes]
rs5997902	0.81[EUR][1000 genomes]
rs5997912	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5997913	0.80[EUR][1000 genomes]
rs5997933	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5997939	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5997949	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71324184	0.91[EUR][1000 genomes]
rs714909	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs715510	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7287267	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7293171	0.82[EUR][1000 genomes]
rs737684	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs737887	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737888	0.84[EUR][1000 genomes]
rs8135344	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8135347	0.81[EUR][1000 genomes]
rs8138596	0.89[EUR][1000 genomes]
rs8141150	0.83[EUR][1000 genomes]
rs9606830	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9606831	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9606839	0.83[EUR][1000 genomes]
rs9609257	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9609264	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609265	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609266	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609267	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9609268	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9609276	0.82[EUR][1000 genomes]
rs9609277	0.83[EUR][1000 genomes]
rs9621235	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058844	chr22:31597104-31725296	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv834176	chr22:31682426-31864701	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
3	esv3333136	chr22:31704947-31758417	Active TSS Flanking Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9609254	DRG1	Cis_1M	lymphoblastoid	RTeQTL
rs9609254	SFI1	cis	Thyroid	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:31689400-31709000	Weak transcription	Placenta	Placenta
2	chr22:31692600-31709200	Weak transcription	Stomach Mucosa	stomach
3	chr22:31693400-31709200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr22:31693800-31720000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr22:31697000-31709400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr22:31698000-31709200	Weak transcription	Adipose Nuclei	Adipose
7	chr22:31698400-31709200	Weak transcription	Fetal Intestine Small	intestine
8	chr22:31702200-31709400	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr22:31703000-31709200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr22:31703200-31706400	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr22:31704200-31709200	Weak transcription	Stomach Smooth Muscle	stomach
12	chr22:31704800-31708800	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr22:31704800-31709000	Weak transcription	Primary T cells from cord blood	blood
14	chr22:31704800-31709000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr22:31704800-31709200	Weak transcription	Primary B cells from peripheral blood	blood
16	chr22:31704800-31711400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr22:31704800-31711600	Weak transcription	Primary B cells from cord blood	blood
18	chr22:31704800-31720200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr22:31705000-31708800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr22:31705000-31709000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr22:31705400-31707600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr22:31705600-31706200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr22:31705600-31709000	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr22:31705600-31709000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
25	chr22:31705800-31709000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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