Variant report

Variant	rs4768142
Chromosome Location	chr12:47568721-47568722
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	chr12:47564847..47568239-chr12:47568410..47570337,3	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10785664	1.00[YRI][hapmap]
rs10785665	1.00[YRI][hapmap]
rs10785668	1.00[YRI][hapmap]
rs10881045	0.81[CEU][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes]
rs10881047	0.89[AMR][1000 genomes]
rs10881069	1.00[YRI][hapmap]
rs10881070	1.00[YRI][hapmap]
rs11183738	0.81[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes]
rs11183740	0.93[AMR][1000 genomes]
rs11183741	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs11183744	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs11183750	1.00[YRI][hapmap]
rs11183751	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs11183752	0.81[CEU][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs11183759	0.80[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11183760	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11183761	0.81[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11183776	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11183777	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183779	0.85[CEU][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs11183783	0.84[CEU][hapmap];1.00[YRI][hapmap]
rs12368600	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12370192	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12370851	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs1554693	1.00[YRI][hapmap]
rs17222290	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17821774	0.84[ASW][hapmap];1.00[YRI][hapmap]
rs1917655	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs1917657	1.00[ASW][hapmap];0.81[CEU][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs2408718	0.84[ASW][hapmap]
rs35456925	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768143	1.00[YRI][hapmap]
rs4768779	1.00[YRI][hapmap]
rs4768781	1.00[YRI][hapmap]
rs4768782	1.00[YRI][hapmap]
rs73101453	0.96[AMR][1000 genomes]
rs73108103	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73108123	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs732523	0.84[ASW][hapmap]
rs7974410	0.84[ASW][hapmap]
rs832729	0.89[CEU][hapmap]
rs952967	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469368	chr12:47374908-47675680	Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv558784	chr12:47374908-47675680	Genic enhancers Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv832399	chr12:47502910-47689601	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2751100	chr12:47541390-47746157	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4768142	HDAC7	cis	parietal	SCAN
rs4768142	DNAJC22	cis	cerebellum	SCAN
rs4768142	CCDC65	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47536000-47578000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr12:47550600-47571800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr12:47550600-47582400	Weak transcription	Aorta	Aorta
4	chr12:47550800-47570000	Weak transcription	Colon Smooth Muscle	Colon
5	chr12:47550800-47570200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr12:47551200-47583600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr12:47554800-47579600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr12:47555000-47576400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr12:47556800-47570400	Weak transcription	Stomach Smooth Muscle	stomach
10	chr12:47557800-47581600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr12:47558600-47580200	Weak transcription	Primary B cells from cord blood	blood
12	chr12:47558800-47570000	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr12:47558800-47582200	Weak transcription	NH-A	brain
14	chr12:47558800-47582400	Weak transcription	Lung	lung
15	chr12:47559000-47570200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr12:47559000-47578000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr12:47559000-47582200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr12:47559400-47570800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr12:47560200-47570000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr12:47560200-47578800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr12:47561400-47578000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr12:47566400-47568800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:47566600-47568800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr12:47566600-47575600	Weak transcription	A549	lung
25	chr12:47566600-47582400	Weak transcription	HSMM	muscle
26	chr12:47566800-47570000	Weak transcription	Primary T cells from cord blood	blood
27	chr12:47567000-47570800	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr12:47568000-47575800	Weak transcription	Primary B cells from peripheral blood	blood
29	chr12:47568200-47580800	Weak transcription	Primary T helper cells fromperipheralblood	blood

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