Variant report

Variant	rs6508915
Chromosome Location	chr19:40347658-40347659
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:40345236..40348068-chr19:40350382..40353367,3	K562	blood:
2	chr19:40335334..40338693-chr19:40343842..40347781,4	K562	blood:
3	chr19:40343735..40346295-chr19:40347078..40349470,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105202	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10048486	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1007919	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1017130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10404641	0.80[CHB][hapmap]
rs10422383	0.94[CHB][hapmap];0.92[JPT][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10423671	0.80[CHB][hapmap]
rs11666032	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1476920	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1476921	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1541534	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1541535	0.86[CEU][hapmap];0.88[CHB][hapmap];0.91[JPT][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2110232	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2354796	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.89[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2354797	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2354798	0.84[AFR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2354799	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35433569	0.81[ASN][1000 genomes]
rs3760928	0.89[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7251846	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7252868	0.80[CHB][hapmap];0.90[GIH][hapmap]
rs7508451	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3329492	chr19:40198535-40437035	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	esv2758498	chr19:40227904-40521130	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv2758760	chr19:40227904-40521130	Genic enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv428022	chr19:40227904-40521130	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
5	nsv9725	chr19:40315519-40412523	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv2483	chr19:40340641-40435505	Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv510766	chr19:40344356-40453018	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6508915	CIC	cis	parietal	SCAN
rs6508915	PSMC4	cis	lymphoblastoid	seeQTL
rs6508915	ZNF404	cis	parietal	SCAN
rs6508915	SPTAN1	trans	cerebellum	SCAN
rs6508915	FOSB	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
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