Variant report

Variant	rs4343997
Chromosome Location	chr7:3362918-3362919
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	chr7:3339157..3341924-chr7:3361736..3363341,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000146555	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10499328	0.95[YRI][hapmap]
rs1522502	0.84[TSI][hapmap]
rs1525553	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1525554	0.91[ASW][hapmap];0.91[CEU][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17133289	0.83[CEU][hapmap];0.81[LWK][hapmap];0.87[MKK][hapmap];0.91[YRI][hapmap]
rs17133292	0.80[GIH][hapmap];0.80[TSI][hapmap]
rs17133300	0.80[TSI][hapmap]
rs17133341	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs17133346	0.83[CEU][hapmap];0.87[EUR][1000 genomes]
rs17133355	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs17133370	0.91[CEU][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs17133379	0.91[CEU][hapmap];0.89[TSI][hapmap]
rs17133405	0.84[TSI][hapmap]
rs17133409	0.85[TSI][hapmap]
rs1880608	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2341582	0.87[EUR][1000 genomes]
rs28633216	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4326295	0.91[CEU][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4418248	0.91[ASW][hapmap];0.84[TSI][hapmap];0.95[YRI][hapmap]
rs56142232	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56143924	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56806161	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs57893579	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs58608495	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs58713621	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs59365175	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59604371	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59719823	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6462005	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66819701	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs68100835	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6945059	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6955831	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6963701	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs6978143	0.91[CEU][hapmap];0.94[YRI][hapmap]
rs73036754	0.82[EUR][1000 genomes]
rs73044757	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73044792	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73044797	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73046637	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73046678	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73046696	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73048618	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73288374	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73292178	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73672091	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73672093	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73675313	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7459157	0.91[CEU][hapmap]
rs7779576	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7780037	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7780894	0.94[YRI][hapmap]
rs7781736	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7788172	0.91[CEU][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7796564	0.91[CEU][hapmap]
rs7799163	0.91[CEU][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7799969	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7801995	0.87[EUR][1000 genomes]
rs7807993	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs7810155	0.83[CEU][hapmap]
rs7811986	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9691979	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9969312	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023127	chr7:3216344-3466223	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1018173	chr7:3258989-3879848	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv538660	chr7:3258989-3879848	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2758100	chr7:3286625-3560229	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv2759500	chr7:3286625-3560229	Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1016555	chr7:3298478-3872512	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv538661	chr7:3298478-3872512	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1019515	chr7:3300048-3479972	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv887324	chr7:3308195-3400105	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv605892	chr7:3341589-3424878	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv1020764	chr7:3348458-3554820	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv538662	chr7:3348458-3554820	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv981785	chr7:3353184-3367204	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv1019492	chr7:3359294-3479972	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
15	nsv538663	chr7:3359294-3479972	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
16	esv2757204	chr7:3359491-3460355	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4343997	SDK1	cis	Whole Blood	GTEx
rs4343997	SDK1	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3344600-3366600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr7:3350200-3366800	Weak transcription	Fetal Brain Male	brain
3	chr7:3358800-3366800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr7:3359000-3385800	Weak transcription	Pancreas	Pancrea
5	chr7:3360600-3364600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr7:3362200-3363000	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr7:3362400-3363000	ZNF genes & repeats	Aorta	Aorta

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