Variant report

Variant	rs12052046
Chromosome Location	chr19:39135874-39135875
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39127830..39130773-chr19:39133940..39135979,2	K562	blood:
2	chr19:39127810..39130773-chr19:39133940..39135979,3	K562	blood:
3	chr19:39131572..39135993-chr19:39136414..39138889,4	K562	blood:
4	chr19:39129454..39131197-chr19:39135431..39138109,2	MCF-7	breast:
5	chr19:39135827..39140696-chr19:39337712..39343036,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000130402	Chromatin interaction
ENSG00000104824	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11553600	0.84[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.92[MKK][hapmap];1.00[ASN][1000 genomes]
rs17589415	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17665451	0.83[CEU][hapmap];1.00[CHB][hapmap];0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17708009	1.00[CHB][hapmap]
rs2228068	1.00[CHB][hapmap]
rs2368476	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs41482151	0.84[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];0.83[LWK][hapmap];0.92[MKK][hapmap];0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs45468197	1.00[ASN][1000 genomes]
rs4616403	1.00[ASN][1000 genomes]
rs4802744	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4802747	0.84[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.82[LWK][hapmap];0.92[MKK][hapmap];1.00[ASN][1000 genomes]
rs4802775	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs67438539	1.00[ASN][1000 genomes]
rs67953948	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7246615	0.82[ASW][hapmap]
rs7254832	1.00[CHB][hapmap]
rs7258075	1.00[CHB][hapmap]
rs7258742	1.00[ASN][1000 genomes]
rs73032668	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73032691	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73032697	1.00[ASN][1000 genomes]
rs73034621	1.00[ASN][1000 genomes]
rs73038909	1.00[ASN][1000 genomes]
rs73038918	1.00[ASN][1000 genomes]
rs73038924	1.00[ASN][1000 genomes]
rs73038930	1.00[ASN][1000 genomes]
rs73038936	1.00[ASN][1000 genomes]
rs73038948	1.00[ASN][1000 genomes]
rs7351086	0.83[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];0.90[MKK][hapmap];1.00[ASN][1000 genomes]
rs8103824	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs8182484	1.00[ASN][1000 genomes]
rs888995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[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	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833826	chr19:38945106-39184547	Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv833827	chr19:38993054-39184547	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv833828	chr19:39084759-39257979	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
6	nsv1057901	chr19:39112486-39174332	Genic enhancers Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases
7	nsv911667	chr19:39119898-39143289	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS 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	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs12052046	CADM4	cis	cerebellum	SCAN
rs12052046	ZNF234	cis	parietal	SCAN
rs12052046	ZC3H4	cis	parietal	SCAN
rs12052046	LYPD3	cis	cerebellum	SCAN
rs12052046	KCNK6	cis	lymphoblastoid	seeQTL
rs12052046	CAPN12	cis	lymphoblastoid	seeQTL
rs12052046	TMEM145	cis	parietal	SCAN
rs12052046	ZNF526	cis	cerebellum	SCAN
rs12052046	ATP1A3	cis	parietal	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39120800-39137800	Weak transcription	Fetal Brain Male	brain
2	chr19:39123800-39137800	Weak transcription	Ovary	ovary
3	chr19:39126200-39138200	Weak transcription	Psoas Muscle	Psoas
4	chr19:39126400-39138200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr19:39126600-39138400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr19:39126800-39136600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr19:39126800-39137800	Weak transcription	Brain Substantia Nigra	brain
8	chr19:39126800-39137800	Weak transcription	Fetal Lung	lung
9	chr19:39126800-39137800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr19:39127000-39137800	Weak transcription	Fetal Kidney	kidney
11	chr19:39127400-39137800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr19:39127400-39137800	Weak transcription	Brain Hippocampus Middle	brain
13	chr19:39127400-39137800	Weak transcription	Osteobl	bone
14	chr19:39127400-39138200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr19:39127600-39137600	Weak transcription	Brain Angular Gyrus	brain
16	chr19:39127600-39137800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr19:39127600-39137800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr19:39127600-39137800	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr19:39127600-39137800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr19:39127600-39137800	Weak transcription	Colon Smooth Muscle	Colon
21	chr19:39127600-39138200	Weak transcription	HSMM	muscle
22	chr19:39127600-39138400	Weak transcription	Aorta	Aorta
23	chr19:39127800-39137800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr19:39127800-39137800	Weak transcription	Fetal Brain Female	brain
25	chr19:39128000-39136600	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr19:39128000-39137600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr19:39128000-39137600	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr19:39128000-39137600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr19:39128000-39137600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr19:39128000-39137600	Weak transcription	Fetal Thymus	thymus
31	chr19:39128000-39137600	Weak transcription	Dnd41	blood
32	chr19:39128000-39137800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr19:39128000-39137800	Weak transcription	NHLF	lung
34	chr19:39128000-39138200	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr19:39128000-39138200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr19:39128200-39137600	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr19:39128400-39136600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr19:39128400-39137600	Weak transcription	Primary B cells from peripheral blood	blood
39	chr19:39128400-39137600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr19:39128400-39137600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr19:39128400-39137600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr19:39128400-39137600	Weak transcription	K562	blood
43	chr19:39128400-39138400	Weak transcription	Primary T cells from cord blood	blood
44	chr19:39129200-39137600	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr19:39129400-39136600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr19:39129400-39137800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr19:39129400-39137800	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr19:39129600-39137800	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr19:39129600-39137800	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr19:39129800-39137600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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