Variant report

Variant	rs4502340
Chromosome Location	chr19:40851071-40851072
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:40846921..40852460-chr19:40852861..40856555,6	K562	blood:

Variant related genes	Relation type
ENSG00000160392	Chromatin interaction
ENSG00000105223	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs11083554	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs12151335	0.85[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12459567	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12460555	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes]
rs12460615	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12977474	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12985477	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16974196	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs1962639	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1991460	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2304186	0.89[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.87[TSI][hapmap]
rs2368575	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs33933140	0.89[CEU][hapmap];0.86[CHB][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.87[TSI][hapmap]
rs34894858	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs35562135	0.81[EUR][1000 genomes]
rs3745195	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3746006	0.81[JPT][hapmap]
rs4479364	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4490097	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4524046	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4802072	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4802076	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs4803324	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4803325	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4803326	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4803327	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4803328	0.87[ASN][1000 genomes]
rs55710016	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57158010	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58502633	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59263025	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7259273	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7259541	0.85[JPT][hapmap]
rs73046335	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7507651	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7508513	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8110323	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs890773	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs892117	0.82[CHB][hapmap];0.91[JPT][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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4502340	TMEM91	cis	parietal	SCAN
rs4502340	VASP	cis	cerebellum	SCAN
rs4502340	SLC1A5	cis	parietal	SCAN
rs4502340	ERCC1	cis	parietal	SCAN
rs4502340	DMRTC2	cis	parietal	SCAN
rs4502340	PLAUR	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40826600-40853000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr19:40832200-40852800	Weak transcription	NHDF-Ad	bronchial
3	chr19:40834400-40853400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr19:40834800-40853600	Weak transcription	Small Intestine	intestine
5	chr19:40836000-40853600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr19:40837400-40853400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr19:40837400-40853600	Weak transcription	Stomach Mucosa	stomach
8	chr19:40839800-40852800	Weak transcription	Hela-S3	cervix
9	chr19:40839800-40853400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr19:40840000-40852800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr19:40840000-40852800	Weak transcription	HUVEC	blood vessel
12	chr19:40840000-40853400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr19:40840000-40853600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr19:40840200-40852800	Weak transcription	HepG2	liver
15	chr19:40840400-40852800	Weak transcription	Fetal Kidney	kidney
16	chr19:40840400-40853000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr19:40840400-40853000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr19:40840400-40853000	Weak transcription	Fetal Brain Male	brain
19	chr19:40840400-40853400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr19:40841400-40853000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr19:40842200-40852800	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr19:40842200-40853200	Weak transcription	Primary B cells from peripheral blood	blood
23	chr19:40842200-40853600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr19:40842200-40853600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr19:40842400-40852800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr19:40842400-40853000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr19:40842400-40853000	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr19:40842400-40853400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr19:40842400-40853600	Weak transcription	Fetal Intestine Large	intestine
30	chr19:40842400-40853600	Weak transcription	Ovary	ovary
31	chr19:40842600-40853400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr19:40842800-40853000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr19:40842800-40853600	Weak transcription	Pancreas	Pancrea
34	chr19:40843000-40853000	Weak transcription	NH-A	brain
35	chr19:40843000-40853400	Weak transcription	Rectal Smooth Muscle	rectum
36	chr19:40845400-40852800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr19:40845400-40853000	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr19:40845400-40853200	Weak transcription	Primary hematopoietic stem cells	blood
39	chr19:40845600-40852800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr19:40845600-40852800	Weak transcription	Liver	Liver
41	chr19:40845600-40852800	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr19:40845600-40853000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr19:40845600-40853200	Weak transcription	Primary B cells from cord blood	blood
44	chr19:40845600-40853400	Weak transcription	Fetal Lung	lung
45	chr19:40846000-40852800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr19:40846000-40853000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr19:40846200-40852800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr19:40846200-40853000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr19:40846200-40853400	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr19:40846400-40852600	Weak transcription	Cortex derived primary cultured neurospheres	brain

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