Variant report

Variant	rs4802074
Chromosome Location	chr19:40848081-40848082
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:40846573..40849159-chr19:40852803..40855284,3	K562	blood:
2	chr19:40787579..40789839-chr19:40846986..40849835,2	MCF-7	breast:
3	chr19:40846921..40852460-chr19:40852861..40856555,6	K562	blood:

Variant related genes	Relation type
ENSG00000105221	Chromatin interaction
ENSG00000105223	Chromatin interaction
ENSG00000207631	Chromatin interaction
ENSG00000160392	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10402740	0.89[CHB][hapmap];0.85[JPT][hapmap];0.86[LWK][hapmap];0.94[MEX][hapmap]
rs10414431	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1129156	0.87[MEX][hapmap]
rs11668242	0.85[CHB][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];0.87[ASN][1000 genomes]
rs11880261	0.82[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.80[TSI][hapmap]
rs12609706	0.87[ASN][1000 genomes]
rs12974529	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12981110	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2304184	0.87[MEX][hapmap]
rs339526	0.87[MEX][hapmap]
rs3730050	1.00[ASW][hapmap];0.82[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap];0.81[YRI][hapmap]
rs3730051	1.00[ASW][hapmap];0.90[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap]
rs4239504	0.85[JPT][hapmap];0.87[MEX][hapmap]
rs4239506	0.84[AFR][1000 genomes]
rs4257318	0.90[ASW][hapmap];0.83[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4337402	0.83[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4490099	0.90[ASW][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs4499338	0.82[AFR][1000 genomes]
rs4558508	1.00[ASW][hapmap];0.82[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap]
rs4802070	0.87[MEX][hapmap]
rs4802071	0.82[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap]
rs4802073	0.83[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4803320	1.00[ASW][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.84[TSI][hapmap]
rs6508936	0.82[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs7248338	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7249146	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]
rs7250897	1.00[ASW][hapmap];0.82[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.81[YRI][hapmap]
rs7255581	0.87[ASN][1000 genomes]
rs7257972	0.83[CEU][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7260106	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7260517	1.00[ASW][hapmap];0.82[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.81[YRI][hapmap]
rs7508604	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8100018	0.95[JPT][hapmap]
rs8102171	0.82[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap]
rs8110888	0.83[CEU][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs969531	1.00[ASW][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap];0.81[YRI][hapmap]

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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4802074	C19orf47	cis	lymphoblastoid	seeQTL
rs4802074	PTGIR	cis	parietal	SCAN
rs4802074	BLVRB	cis	multi-tissue	Pritchard
rs4802074	APOE	cis	cerebellum	SCAN
rs4802074	PPP1R13L	cis	cerebellum	SCAN
rs4802074	C19orf47	cis	multi-tissue	Pritchard
rs4802074	EMP3	cis	cerebellum	SCAN
rs4802074	FLJ36888	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40820800-40848400	Strong transcription	Dnd41	blood
2	chr19:40822000-40851000	Strong transcription	Fetal Stomach	stomach
3	chr19:40824200-40848600	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr19:40824200-40849600	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr19:40826600-40853000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr19:40832200-40852800	Weak transcription	NHDF-Ad	bronchial
7	chr19:40834400-40853400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr19:40834800-40853600	Weak transcription	Small Intestine	intestine
9	chr19:40836000-40853600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr19:40837200-40848400	Weak transcription	Psoas Muscle	Psoas
11	chr19:40837400-40853400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr19:40837400-40853600	Weak transcription	Stomach Mucosa	stomach
13	chr19:40839800-40852800	Weak transcription	Hela-S3	cervix
14	chr19:40839800-40853400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr19:40840000-40852800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr19:40840000-40852800	Weak transcription	HUVEC	blood vessel
17	chr19:40840000-40853400	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr19:40840000-40853600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr19:40840200-40850400	Weak transcription	Osteobl	bone
20	chr19:40840200-40852800	Weak transcription	HepG2	liver
21	chr19:40840400-40850800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr19:40840400-40852800	Weak transcription	Fetal Kidney	kidney
23	chr19:40840400-40853000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr19:40840400-40853000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr19:40840400-40853000	Weak transcription	Fetal Brain Male	brain
26	chr19:40840400-40853400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr19:40841400-40853000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr19:40842200-40848600	Weak transcription	Gastric	stomach
29	chr19:40842200-40852800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr19:40842200-40853200	Weak transcription	Primary B cells from peripheral blood	blood
31	chr19:40842200-40853600	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr19:40842200-40853600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr19:40842400-40848800	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr19:40842400-40849000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr19:40842400-40850600	Weak transcription	Brain Substantia Nigra	brain
36	chr19:40842400-40852800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr19:40842400-40853000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr19:40842400-40853000	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr19:40842400-40853400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr19:40842400-40853600	Weak transcription	Fetal Intestine Large	intestine
41	chr19:40842400-40853600	Weak transcription	Ovary	ovary
42	chr19:40842600-40853400	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr19:40842800-40848400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr19:40842800-40850400	Weak transcription	Esophagus	oesophagus
45	chr19:40842800-40853000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr19:40842800-40853600	Weak transcription	Pancreas	Pancrea
47	chr19:40843000-40850400	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr19:40843000-40853000	Weak transcription	NH-A	brain
49	chr19:40843000-40853400	Weak transcription	Rectal Smooth Muscle	rectum
50	chr19:40844000-40848400	Weak transcription	Spleen	Spleen

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