Variant report

Variant	rs10422343
Chromosome Location	chr19:40854801-40854802
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:161)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:161 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TBL1XR1	chr19:40854068-40854858	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:40854021-40854828	GM18526	blood:	n/a	n/a
3	IRF1	chr19:40853820-40855040	K562	blood:	n/a	n/a
4	MAX	chr19:40853935-40854907	HepG2	liver:	n/a	n/a
5	POLR2A	chr19:40854398-40854862	U87	brain:	n/a	n/a
6	POLR2A	chr19:40853832-40855318	K562	blood:	n/a	n/a
7	POLR2A	chr19:40854045-40854867	HEK293	kidney:	n/a	n/a
8	USF1	chr19:40853761-40855378	A549	lung:	n/a	chr19:40854419-40854430
9	TEAD4	chr19:40853795-40855021	K562	blood:	n/a	n/a
10	POLR2A	chr19:40854074-40854825	HCT-116	colon:	n/a	n/a
11	IRF1	chr19:40854093-40855178	K562	blood:	n/a	n/a
12	TCF12	chr19:40853672-40855441	A549	lung:	n/a	n/a
13	MAX	chr19:40854089-40854874	SK-N-SH	brain:	n/a	n/a
14	POLR2A	chr19:40853848-40854974	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr19:40853992-40854916	Gliobla	brain:	n/a	n/a
16	POLR2A	chr19:40854042-40854850	GM12892	blood:	n/a	n/a
17	POLR2A	chr19:40853983-40854933	PFSK-1	brain:	n/a	n/a
18	TAF1	chr19:40854113-40854840	ECC-1	luminal epithelium:	n/a	n/a
19	NFIC	chr19:40854109-40854842	GM12878	blood:	n/a	n/a
20	MAX	chr19:40853509-40855470	A549	lung:	n/a	n/a
21	POLR2A	chr19:40854061-40854884	HUVEC	blood vessel:	n/a	n/a
22	POLR2A	chr19:40853883-40854904	H1-neurons	neurons:	n/a	n/a
23	SIN3A	chr19:40853669-40855017	GM12878	blood:	n/a	chr19:40854213-40854226
24	POLR2A	chr19:40854031-40854848	GM18505	blood:	n/a	n/a
25	MAX	chr19:40854169-40855294	A549	lung:	n/a	n/a
26	RFX5	chr19:40854015-40855213	Hela-S3	cervix:	n/a	chr19:40855055-40855072 chr19:40854526-40854535
27	POLR2A	chr19:40854428-40854801	HepG2	liver:	n/a	n/a
28	POLR2A	chr19:40853960-40854872	GM12891	blood:	n/a	n/a
29	MAZ	chr19:40853622-40855561	IMR90	lung:	n/a	n/a
30	POLR2A	chr19:40853983-40854935	HUVEC	blood vessel:	n/a	n/a
31	POLR2A	chr19:40853925-40855585	H1-neurons	neurons:	n/a	n/a
32	CREB1	chr19:40854053-40855389	GM12878	blood:	n/a	chr19:40855171-40855184
33	POLR2A	chr19:40853987-40854890	MCF-7	breast:	n/a	n/a
34	RCOR1	chr19:40853890-40855199	K562	blood:	n/a	n/a
35	POLR2A	chr19:40853990-40854829	GM12878	blood:	n/a	n/a
36	USF1	chr19:40853788-40855348	A549	lung:	n/a	chr19:40854419-40854430
37	MXI1	chr19:40854037-40855141	K562	blood:	n/a	n/a
38	POLR2A	chr19:40854029-40854847	GM19099	blood:	n/a	n/a
39	POLR2A	chr19:40853882-40854958	SK-N-MC	brain:	n/a	n/a
40	POLR2A	chr19:40854019-40854911	MCF-7	breast:	n/a	n/a
41	POLR2A	chr19:40854046-40854922	GM12878	blood:	n/a	n/a
42	POLR2A	chr19:40854035-40854836	GM19193	blood:	n/a	n/a
43	SIN3AK20	chr19:40853923-40855127	K562	blood:	n/a	n/a
44	HEY1	chr19:40853999-40854850	HepG2	liver:	n/a	n/a
45	POLR2A	chr19:40854016-40855293	MCF10A-Er-Src	breast:	n/a	n/a
46	TCF12	chr19:40854029-40854877	ECC-1	luminal epithelium:	n/a	n/a
47	USF1	chr19:40854113-40854811	SK-N-SH	brain:	n/a	chr19:40854419-40854430
48	SIN3AK20	chr19:40853815-40855463	A549	lung:	n/a	n/a
49	POLR2A	chr19:40853965-40855274	PBDE	blood:	n/a	n/a
50	POLR2A	chr19:40853917-40854919	GM12878	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:40846921..40852460-chr19:40852861..40856555,6	K562	blood:
2	chr19:40853951..40856077-chr19:40931313..40932883,2	MCF-7	breast:
3	chr19:40853192..40856646-chr19:40870044..40873206,4	K562	blood:
4	chr19:40853841..40855507-chr19:41105833..41108523,2	K562	blood:
5	chr19:40853028..40855563-chr19:40876148..40878218,2	K562	blood:
6	chr19:40853787..40856715-chr19:40882110..40885015,2	K562	blood:
7	chr19:40852692..40855852-chr19:40948280..40952207,5	K562	blood:
8	chr19:40853920..40856703-chr19:40862603..40866302,4	K562	blood:
9	chr19:40846573..40849159-chr19:40852803..40855284,3	K562	blood:
10	chr19:40853029..40856025-chr19:41082472..41085390,2	K562	blood:
11	chr19:40851266..40855955-chr19:40945466..40950850,6	K562	blood:

No data

Variant related genes	Relation type
C19orf47	TF binding region
ENSG00000167565	Chromatin interaction
ENSG00000160410	Chromatin interaction
ENSG00000206925	Chromatin interaction
ENSG00000090006	Chromatin interaction
ENSG00000197019	Chromatin interaction
ENSG00000105223	Chromatin interaction
ENSG00000160392	Chromatin interaction
ENSG00000268366	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10408356	0.92[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10415181	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10416620	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10418932	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10419465	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10420842	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10423896	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12151243	0.92[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16974157	0.81[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2163840	0.84[ASN][1000 genomes]
rs2304188	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.87[TSI][hapmap];0.80[EUR][1000 genomes]
rs28667591	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34716810	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55862427	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57804337	0.87[ASN][1000 genomes]
rs57885763	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58336440	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58613082	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59010363	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60869669	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61685259	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62107590	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62107593	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62107594	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62107630	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62107631	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7247916	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7248012	0.83[ASN][1000 genomes]
rs7248861	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7254617	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8100207	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8111619	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8112998	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs892118	0.85[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs892119	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs892120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9304588	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9304589	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs934426	0.85[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.87[TSI][hapmap];0.80[EUR][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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10422343	PSG8	cis	parietal	SCAN
rs10422343	APOC4	cis	cerebellum	SCAN
rs10422343	EML2	cis	cerebellum	SCAN
rs10422343	RPL18	cis	parietal	SCAN
rs10422343	DEDD2	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40852800-40855200	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr19:40852800-40855200	Active TSS	iPS-18 Cell Line	embryonic stem cell
3	chr19:40852800-40855200	Active TSS	NHDF-Ad	bronchial
4	chr19:40852800-40855600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr19:40852800-40855600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr19:40853000-40855000	Active TSS	NH-A	brain
7	chr19:40853000-40855200	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr19:40853000-40855200	Active TSS	HSMM	muscle
9	chr19:40853000-40855800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr19:40853200-40855000	Active TSS	HMEC	breast
11	chr19:40853200-40855200	Active TSS	GM12878-XiMat	blood
12	chr19:40853200-40855200	Active TSS	K562	blood
13	chr19:40853200-40855200	Active TSS	NHLF	lung
14	chr19:40853200-40855400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr19:40853400-40855000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr19:40853400-40855000	Active TSS	Fetal Lung	lung
17	chr19:40853400-40855000	Active TSS	Rectal Mucosa Donor 31	rectum
18	chr19:40853400-40855000	Active TSS	HSMMtube	muscle
19	chr19:40853400-40855200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr19:40853400-40855200	Active TSS	Fetal Muscle Trunk	muscle
21	chr19:40853400-40855400	Active TSS	H1 Cell Line	embryonic stem cell
22	chr19:40853400-40855600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr19:40853400-40855600	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr19:40853400-40855600	Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr19:40853600-40855000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr19:40853600-40855000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr19:40853600-40855000	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr19:40853600-40855200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr19:40853600-40855200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr19:40853600-40855200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr19:40853600-40855200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr19:40853600-40855200	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr19:40853600-40855200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr19:40853600-40855200	Active TSS	Fetal Intestine Small	intestine
35	chr19:40853600-40855200	Active TSS	Left Ventricle	heart
36	chr19:40853600-40855200	Active TSS	Lung	lung
37	chr19:40853600-40855200	Active TSS	Ovary	ovary
38	chr19:40853600-40855200	Active TSS	Pancreas	Pancrea
39	chr19:40853600-40855200	Active TSS	Right Ventricle	heart
40	chr19:40853600-40855200	Active TSS	Small Intestine	intestine
41	chr19:40853600-40855200	Active TSS	A549	lung
42	chr19:40853600-40855400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
43	chr19:40853600-40855400	Active TSS	H9 Cell Line	embryonic stem cell
44	chr19:40853600-40855400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr19:40853600-40855400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
46	chr19:40853600-40855400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr19:40853600-40855400	Active TSS	Aorta	Aorta
48	chr19:40853600-40855400	Active TSS	Fetal Brain Female	brain
49	chr19:40853600-40855400	Active TSS	Psoas Muscle	Psoas
50	chr19:40853600-40855600	Active TSS	ES-I3 Cell Line	embryonic stem cell

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