Variant report

Variant	rs2396374
Chromosome Location	chr6:44993041-44993042
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:44987589..44991130-chr6:44992558..44996333,3	K562	blood:

Extended variants
information (count: 84 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10080909	0.89[EUR][1000 genomes]
rs10498757	1.00[ASN][1000 genomes]
rs13436998	0.82[YRI][hapmap]
rs16872751	1.00[CHB][hapmap];0.94[YRI][hapmap];0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16873056	0.82[CEU][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16873073	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16873103	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16873150	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16873215	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs17209608	0.82[CEU][hapmap]
rs28463085	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs28843161	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs59606274	0.88[AFR][1000 genomes]
rs6925770	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73438898	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73441120	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs73441122	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs73441130	0.85[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs73442933	0.90[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73443219	0.89[AFR][1000 genomes]
rs73443229	0.89[AFR][1000 genomes]
rs73443286	0.89[AFR][1000 genomes]
rs73444966	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73444983	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73447073	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73447433	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73448343	1.00[ASN][1000 genomes]
rs73451303	0.88[EUR][1000 genomes]
rs7742332	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7749796	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7751298	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7762957	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs7768241	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9296447	0.94[YRI][hapmap];0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9296450	0.83[MKK][hapmap];1.00[YRI][hapmap]
rs9296451	1.00[CEU][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9463046	1.00[CHB][hapmap];0.80[LWK][hapmap];0.88[MKK][hapmap];1.00[ASN][1000 genomes]
rs9463053	0.87[AFR][1000 genomes]
rs9463056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9463058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9463066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs9463071	0.88[EUR][1000 genomes]
rs9463079	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9472372	1.00[ASN][1000 genomes]
rs9472373	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9472374	1.00[CHB][hapmap];0.85[LWK][hapmap];0.92[MKK][hapmap];1.00[ASN][1000 genomes]
rs9472375	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9472377	1.00[CHB][hapmap]
rs9472379	1.00[ASN][1000 genomes]
rs9472381	1.00[CHB][hapmap];0.84[YRI][hapmap];1.00[ASN][1000 genomes]
rs9472384	1.00[CHB][hapmap];0.84[YRI][hapmap];1.00[ASN][1000 genomes]
rs9472390	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9472391	0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9472393	0.88[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9472394	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9472395	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9472412	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9472413	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9472414	1.00[YRI][hapmap]
rs9472421	1.00[CEU][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9472424	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9472427	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs9472433	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9472434	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9472435	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9472436	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9472438	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs9885623	0.89[AFR][1000 genomes];0.85[EUR][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	nsv885861	chr6:44837356-45043618	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv1024370	chr6:44878053-45251451	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	esv2758051	chr6:44879791-45056758	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv2759423	chr6:44879791-45056758	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv885862	chr6:44890760-45083966	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv885863	chr6:44890760-45083966	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv885864	chr6:44890760-45198796	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
10	nsv462938	chr6:44909515-45008779	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv470817	chr6:44909515-45008779	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv603007	chr6:44909515-45008779	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv1023018	chr6:44925393-45152912	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv538212	chr6:44925393-45152912	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv603008	chr6:44958372-45081821	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	esv2762589	chr6:44982992-45044580	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2396374	TAF8	cis	cerebellum	SCAN
rs2396374	KIAA0240	cis	parietal	SCAN
rs2396374	GUCA1B	cis	cerebellum	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:44966400-44993600	Weak transcription	HepG2	liver
2	chr6:44974800-45004600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:44977600-44993800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr6:44981600-44994800	Weak transcription	Aorta	Aorta
5	chr6:44981600-44994800	Weak transcription	Pancreas	Pancrea

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