Variant report

Variant	rs7249146
Chromosome Location	chr19:40853492-40853493
allele	C/T
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	JUN	chr19:40853475-40855517	K562	blood:	n/a	chr19:40854527-40854536 chr19:40855172-40855185 chr19:40854259-40854268
2	ZNF384	chr19:40853376-40853525	K562	blood:	n/a	n/a
3	REST	chr19:40853411-40855742	H1-neurons	neurons:	n/a	chr19:40854213-40854226
4	FOSL2	chr19:40853323-40855470	A549	lung:	n/a	chr19:40854527-40854536 chr19:40854259-40854268
5	MAX	chr19:40853420-40855657	A549	lung:	n/a	n/a
6	MAFK	chr19:40853489-40853700	HepG2	liver:	n/a	chr19:40853555-40853566 chr19:40853555-40853566 chr19:40853550-40853565
7	GABPA	chr19:40853466-40854896	A549	lung:	n/a	chr19:40854690-40854699 chr19:40854580-40854594 chr19:40854577-40854591 chr19:40854258-40854267 chr19:40854580-40854591 chr19:40854214-40854223 chr19:40854582-40854591
8	ZNF384	chr19:40853304-40853698	GM12878	blood:	n/a	n/a
9	SIX5	chr19:40853344-40855578	A549	lung:	n/a	n/a
10	HCFC1	chr19:40853367-40855133	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:40846921..40852460-chr19:40852861..40856555,6	K562	blood:
2	chr19:40853192..40856646-chr19:40870044..40873206,4	K562	blood:
3	chr19:40853028..40855563-chr19:40876148..40878218,2	K562	blood:
4	chr19:40852692..40855852-chr19:40948280..40952207,5	K562	blood:
5	chr19:40846573..40849159-chr19:40852803..40855284,3	K562	blood:
6	chr19:40853029..40856025-chr19:41082472..41085390,2	K562	blood:
7	chr19:40851266..40855955-chr19:40945466..40950850,6	K562	blood:
8	chr19:40788680..40791212-chr19:40852795..40854366,2	K562	blood:

Variant related genes	Relation type
C19orf47	TF binding region
PLD3	TF binding region
ENSG00000160410	Chromatin interaction
ENSG00000160392	Chromatin interaction
ENSG00000268366	Chromatin interaction
ENSG00000206925	Chromatin interaction
ENSG00000167565	Chromatin interaction
ENSG00000105221	Chromatin interaction
ENSG00000105223	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10402740	0.81[JPT][hapmap];0.82[MEX][hapmap]
rs10414431	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1129156	0.95[CHB][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap]
rs11668242	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]
rs11880261	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.88[ASN][1000 genomes]
rs12609706	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2304184	0.95[CHB][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap]
rs2304189	0.89[CHB][hapmap]
rs339526	0.90[CHB][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap]
rs3730050	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.82[ASN][1000 genomes]
rs3730051	0.80[CHB][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap]
rs4239504	0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap]
rs4239506	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4257318	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4277441	0.83[ASN][1000 genomes]
rs4332845	0.83[ASN][1000 genomes]
rs4337402	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4490099	0.87[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap]
rs4499338	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4558508	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.82[ASN][1000 genomes]
rs4802070	0.95[CHB][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap]
rs4802071	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4802073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802074	0.83[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4803320	0.89[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap]
rs6508936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7248338	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7250897	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.86[ASN][1000 genomes]
rs7255581	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7257972	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7260106	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7260517	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.84[ASN][1000 genomes]
rs748236	0.82[ASN][1000 genomes]
rs8100018	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs8102171	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.86[ASN][1000 genomes]
rs8104727	0.83[ASN][1000 genomes]
rs8110888	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs969531	0.87[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.84[ASN][1000 genomes]
rs9749283	0.81[EUR][1000 genomes];0.85[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	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
3	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
4	nsv911706	chr19:40842529-40969203	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	esv2754051	chr19:40848081-40863842	Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs7249146	EMP3	cis	cerebellum	SCAN
rs7249146	C19orf47	cis	multi-tissue	Pritchard
rs7249146	ERCC1	cis	parietal	SCAN
rs7249146	APOE	cis	cerebellum	SCAN
rs7249146	C19orf47	cis	lymphoblastoid	seeQTL
rs7249146	ZNF221	cis	parietal	SCAN
rs7249146	SPACA4	cis	cerebellum	SCAN
rs7249146	TMEM91	cis	parietal	SCAN
rs7249146	SYMPK	cis	cerebellum	SCAN
rs7249146	PPP1R13L	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40834800-40853600	Weak transcription	Small Intestine	intestine
2	chr19:40836000-40853600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr19:40837400-40853600	Weak transcription	Stomach Mucosa	stomach
4	chr19:40840000-40853600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:40842200-40853600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr19:40842200-40853600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr19:40842400-40853600	Weak transcription	Fetal Intestine Large	intestine
8	chr19:40842400-40853600	Weak transcription	Ovary	ovary
9	chr19:40842800-40853600	Weak transcription	Pancreas	Pancrea
10	chr19:40848000-40853600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr19:40848000-40853600	Weak transcription	Colonic Mucosa	Colon
12	chr19:40848000-40853600	Weak transcription	Thymus	Thymus
13	chr19:40848200-40853600	Weak transcription	Fetal Intestine Small	intestine
14	chr19:40848400-40853800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr19:40849600-40853600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr19:40851000-40853600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr19:40851000-40853600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr19:40851000-40853600	Weak transcription	Right Atrium	heart
19	chr19:40851000-40853600	Weak transcription	Right Ventricle	heart
20	chr19:40852600-40853600	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr19:40852600-40853600	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr19:40852800-40853600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr19:40852800-40853600	Enhancers	Brain Anterior Caudate	brain
24	chr19:40852800-40853600	Enhancers	Brain Hippocampus Middle	brain
25	chr19:40852800-40853600	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr19:40852800-40853600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr19:40852800-40853600	Enhancers	Colon Smooth Muscle	Colon
28	chr19:40852800-40853600	Enhancers	Fetal Heart	heart
29	chr19:40852800-40853800	Flanking Active TSS	Dnd41	blood
30	chr19:40852800-40853800	Flanking Active TSS	Hela-S3	cervix
31	chr19:40852800-40854200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr19:40852800-40855200	Active TSS	HUES6 Cell Line	embryonic stem cell
33	chr19:40852800-40855200	Active TSS	iPS-18 Cell Line	embryonic stem cell
34	chr19:40852800-40855200	Active TSS	NHDF-Ad	bronchial
35	chr19:40852800-40855600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr19:40852800-40855600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr19:40853000-40853600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr19:40853000-40853600	Enhancers	Primary T cells fromperipheralblood	blood
39	chr19:40853000-40853600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr19:40853000-40853600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr19:40853000-40853600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr19:40853000-40853600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
43	chr19:40853000-40853600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr19:40853000-40853600	Enhancers	Primary T killer memory cells from peripheral blood	blood
45	chr19:40853000-40853600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr19:40853000-40853600	Enhancers	Fetal Brain Male	brain
47	chr19:40853000-40853600	Enhancers	Fetal Stomach	stomach
48	chr19:40853000-40853600	Enhancers	Spleen	Spleen
49	chr19:40853000-40853800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr19:40853000-40853800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood

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