Variant report

Variant	rs12449324
Chromosome Location	chr17:46223379-46223380
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46210896..46212832-chr17:46222809..46224795,2	MCF-7	breast:
2	chr17:46222057..46223830-chr17:46225566..46227649,2	K562	blood:
3	chr17:46221592..46224484-chr17:46225566..46228411,3	K562	blood:

Extended variants
information (count: 23 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11079811	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11079812	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11868509	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs12449529	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12601412	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12602010	0.89[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs12948653	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12953085	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1316643	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16954750	0.81[YRI][hapmap]
rs17619103	1.00[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2525103	0.84[CEU][hapmap]
rs34130316	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34449497	0.91[ASN][1000 genomes]
rs35371915	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35999311	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7215582	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7221416	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7224648	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]

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	nsv469808	chr17:46049868-46228673	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv482897	chr17:46049868-46228673	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
3	nsv908576	chr17:46147807-46260366	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12449324	ASB16	cis	parietal	SCAN
rs12449324	RPRML	cis	parietal	SCAN
rs12449324	PNPO	cis	parietal	SCAN
rs12449324	PNPO	cis	cerebellum	SCAN
rs12449324	KRT13	cis	parietal	SCAN
rs12449324	NAGLU	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46200400-46236600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr17:46204200-46225200	Weak transcription	Liver	Liver
3	chr17:46210000-46224200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr17:46211200-46231600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr17:46212400-46234800	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr17:46215400-46225400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr17:46216400-46251400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr17:46216600-46235600	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr17:46218000-46224200	Weak transcription	Primary B cells from cord blood	blood
10	chr17:46218200-46224800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr17:46220600-46225600	Strong transcription	Primary T cells from cord blood	blood
12	chr17:46220800-46227200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr17:46220800-46228400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr17:46220800-46249000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr17:46221200-46228000	Weak transcription	Primary B cells from peripheral blood	blood
16	chr17:46221400-46230800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr17:46221600-46225400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr17:46221600-46225400	Weak transcription	Thymus	Thymus
19	chr17:46221600-46225600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr17:46221600-46226800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr17:46221600-46238400	Weak transcription	Fetal Thymus	thymus
22	chr17:46222000-46224400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr17:46222200-46223600	Enhancers	GM12878-XiMat	blood
24	chr17:46222400-46223400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr17:46222400-46223400	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr17:46222600-46223400	Enhancers	Fetal Intestine Small	intestine
27	chr17:46222800-46223400	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr17:46222800-46223600	Enhancers	Fetal Intestine Large	intestine
29	chr17:46222800-46234600	Strong transcription	Primary T helper cells PMA-I stimulated	--
30	chr17:46223200-46225200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr17:46223200-46226600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr17:46223200-46228400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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