Variant report

Variant	rs11668242
Chromosome Location	chr19:40836872-40836873
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr19:40836389-40837581	PANC-1	pancreas:	n/a	n/a
2	GATA3	chr19:40836864-40837710	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:40831185..40834096-chr19:40834501..40837244,2	MCF-7	breast:
2	chr19:40833480..40835017-chr19:40835815..40837638,2	MCF-7	breast:

Variant related genes	Relation type
C19orf47	TF binding region
ENSG00000160392	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs10402740	0.81[JPT][hapmap];0.87[MEX][hapmap]
rs10414431	0.85[ASN][1000 genomes]
rs1129156	0.95[CHB][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap]
rs11880261	0.86[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12609706	0.95[ASN][1000 genomes]
rs12974529	0.84[EUR][1000 genomes]
rs12981110	0.84[EUR][1000 genomes]
rs2304184	0.95[CHB][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap]
rs2304189	0.89[CHB][hapmap]
rs339526	0.90[CHB][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap]
rs3730050	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3730051	0.80[CHB][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap]
rs4239504	0.95[CHB][hapmap];0.90[JPT][hapmap];0.93[MEX][hapmap]
rs4239506	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4257318	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4277441	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4332845	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4337402	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4490099	0.86[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap]
rs4499338	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4558508	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4802070	0.95[CHB][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap]
rs4802071	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4802073	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4802074	0.85[CHB][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];0.87[ASN][1000 genomes]
rs4803320	0.89[CHB][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap]
rs6508936	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7248338	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7249146	0.86[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7250897	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7255581	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7257972	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7260106	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7260517	0.86[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs748236	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7508604	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8100018	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs8102171	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8104727	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8110888	0.86[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs969531	0.82[CEU][hapmap];0.89[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9749283	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv2758499	chr19:40612420-40839520	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Enhancers Active TSS 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 miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv2758761	chr19:40612420-40839520	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	esv1833489	chr19:40722123-40923908	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer 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	35 gene(s)	inside rSNPs	diseases
5	nsv833831	chr19:40796740-40960865	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers 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 lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs11668242	EMP3	cis	cerebellum	SCAN
rs11668242	FLJ36888	cis	multi-tissue	Pritchard
rs11668242	C19orf47	cis	multi-tissue	Pritchard
rs11668242	ERCC1	cis	parietal	SCAN
rs11668242	C19orf47	cis	lymphoblastoid	seeQTL
rs11668242	SYMPK	cis	cerebellum	SCAN
rs11668242	TMEM91	cis	parietal	SCAN
rs11668242	SPACA4	cis	cerebellum	SCAN
rs11668242	APOE	cis	cerebellum	SCAN
rs11668242	ZNF221	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40820800-40848400	Strong transcription	Dnd41	blood
2	chr19:40821400-40846000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr19:40822000-40842400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr19:40822000-40843400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr19:40822000-40851000	Strong transcription	Fetal Stomach	stomach
6	chr19:40822200-40842400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr19:40822200-40842600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:40822200-40843200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr19:40822200-40845400	Strong transcription	Fetal Muscle Leg	muscle
10	chr19:40822400-40846200	Strong transcription	Fetal Muscle Trunk	muscle
11	chr19:40823400-40842400	Strong transcription	Fetal Brain Female	brain
12	chr19:40823400-40845400	Strong transcription	Thymus	Thymus
13	chr19:40824000-40839400	Strong transcription	NHLF	lung
14	chr19:40824000-40842200	Strong transcription	Liver	Liver
15	chr19:40824000-40842400	Strong transcription	Brain Germinal Matrix	brain
16	chr19:40824000-40842600	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr19:40824200-40846400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr19:40824200-40848600	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr19:40824200-40849600	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr19:40824400-40843000	Strong transcription	Fetal Thymus	thymus
21	chr19:40825200-40842800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr19:40825400-40842600	Strong transcription	Duodenum Mucosa	Duodenum
23	chr19:40825600-40842200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr19:40825600-40842400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr19:40825800-40837400	Strong transcription	Colonic Mucosa	Colon
26	chr19:40825800-40838600	Strong transcription	Brain Hippocampus Middle	brain
27	chr19:40825800-40841600	Strong transcription	Right Ventricle	heart
28	chr19:40825800-40842200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr19:40825800-40842200	Strong transcription	Adipose Nuclei	Adipose
30	chr19:40825800-40842400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr19:40825800-40842400	Strong transcription	Sigmoid Colon	Sigmoid Colon
32	chr19:40825800-40842400	Strong transcription	Skeletal Muscle Male	skeletal muscle
33	chr19:40825800-40842600	Strong transcription	Primary T helper cells fromperipheralblood	blood
34	chr19:40825800-40842600	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr19:40825800-40845400	Strong transcription	Stomach Smooth Muscle	stomach
36	chr19:40826000-40840200	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr19:40826000-40840600	Strong transcription	HSMMtube	muscle
38	chr19:40826000-40842200	Strong transcription	Gastric	stomach
39	chr19:40826000-40842400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr19:40826000-40842400	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr19:40826000-40842400	Strong transcription	Fetal Intestine Large	intestine
42	chr19:40826000-40842400	Strong transcription	Left Ventricle	heart
43	chr19:40826000-40842400	Strong transcription	Ovary	ovary
44	chr19:40826400-40840200	Strong transcription	Brain Angular Gyrus	brain
45	chr19:40826400-40842200	Strong transcription	Skeletal Muscle Female	skeletal muscle
46	chr19:40826400-40842400	Strong transcription	HUES64 Cell Line	embryonic stem cell
47	chr19:40826400-40843000	Strong transcription	Primary T cells from cord blood	blood
48	chr19:40826400-40847400	Weak transcription	Right Atrium	heart
49	chr19:40826600-40842000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr19:40826600-40842400	Strong transcription	Primary T helper cells PMA-I stimulated	--

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