Variant report

Variant	rs6461936
Chromosome Location	chr7:26427543-26427544
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:26425982..26428299-chr7:26429554..26431318,2	K562	blood:
2	chr7:26427415..26429605-chr7:26480362..26482553,2	K562	blood:
3	chr7:26422992..26424851-chr7:26426516..26429377,2	K562	blood:
4	chr7:26427307..26429397-chr7:26431461..26434298,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10807832	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10951132	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10951133	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10951134	0.85[CEU][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap];0.93[MEX][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10951135	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10951136	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10951137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12531639	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.93[MEX][hapmap];0.81[TSI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12670965	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12672467	1.00[YRI][hapmap]
rs12674232	1.00[YRI][hapmap]
rs13241375	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17153504	0.82[JPT][hapmap]
rs3193526	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3801887	1.00[YRI][hapmap]
rs41443545	1.00[CEU][hapmap];0.93[GIH][hapmap]
rs6461935	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6950352	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6967677	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7780256	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7780650	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7799362	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9638835	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9639536	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9639538	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9639539	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs966416	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029596	chr7:26302739-26737913	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	nsv538804	chr7:26302739-26737913	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6461936	KIAA0087	cis	parietal	SCAN
rs6461936	CYCS	cis	parietal	SCAN
rs6461936	LOC441204	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:26418600-26436000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr7:26427000-26427600	Enhancers	Fetal Brain Male	brain
3	chr7:26427000-26428400	Enhancers	iPS-20b Cell Line	embryonic stem cell
4	chr7:26427200-26427600	Active TSS	Brain Germinal Matrix	brain
5	chr7:26427200-26428200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr7:26427200-26428200	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr7:26427200-26428400	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr7:26427200-26428400	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr7:26427200-26428400	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr7:26427200-26428400	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr7:26427200-26428400	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr7:26427400-26427600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
13	chr7:26427400-26427800	Enhancers	Fetal Brain Female	brain
14	chr7:26427400-26428000	Enhancers	GM12878-XiMat	blood
15	chr7:26427400-26428200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr7:26427400-26428200	Enhancers	H9 Cell Line	embryonic stem cell
17	chr7:26427400-26428200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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