Variant report

Variant	rs5002233
Chromosome Location	chr7:117847220-117847221
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:117841858..117844215-chr7:117844744..117847374,2	K562	blood:
2	chr7:117842197..117843985-chr7:117846070..117847812,2	MCF-7	breast:
3	chr7:117845682..117847702-chr7:117872075..117874755,2	K562	blood:

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10085904	0.91[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs10226152	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10227326	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10229589	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10241875	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs10252627	0.88[EUR][1000 genomes]
rs10267938	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10487390	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1054032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1061731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10953864	0.85[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs1117254	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11486992	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11543742	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11770353	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11979012	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12112697	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs12537795	0.92[CEU][hapmap];0.81[CHB][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12667103	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12673046	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13224733	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2041527	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs2041528	0.81[EUR][1000 genomes]
rs2058416	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2058417	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2191920	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2402322	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2896242	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3802012	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4141028	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs41900	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41901	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41902	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41905	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41906	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41909	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41910	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs41911	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs41915	0.90[EUR][1000 genomes]
rs41916	0.90[EUR][1000 genomes]
rs41926	0.90[EUR][1000 genomes]
rs41933	0.88[EUR][1000 genomes]
rs41934	0.90[EUR][1000 genomes]
rs41935	0.90[EUR][1000 genomes]
rs41938	0.90[EUR][1000 genomes]
rs41939	0.90[EUR][1000 genomes]
rs41945	0.80[EUR][1000 genomes]
rs41960	0.84[EUR][1000 genomes]
rs6466650	0.84[EUR][1000 genomes]
rs6942513	0.84[CEU][hapmap]
rs6944524	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6946855	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6948096	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6956486	0.83[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs6964911	0.92[CEU][hapmap];0.85[CHB][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6965144	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7779933	0.93[EUR][1000 genomes]
rs7796145	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7796148	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7797855	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7799229	0.92[CEU][hapmap];0.87[JPT][hapmap];0.85[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7806490	0.87[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs917761	0.84[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs9655829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9656260	0.85[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs979652	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9886333	0.82[EUR][1000 genomes]
rs989899	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[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	nsv869971	chr7:117420583-118274149	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
2	nsv889088	chr7:117744660-117913648	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	esv3450079	chr7:117846216-117848114	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs5002233	LSM8	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:117833000-117854000	Weak transcription	HSMM	muscle
2	chr7:117833600-117854000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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