Variant report

Variant	rs890773
Chromosome Location	chr19:40826124-40826125
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	chr19:40825864..40828845-chr19:40848574..40850485,2	K562	blood:

Variant related genes	Relation type
ENSG00000160392	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11083554	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs12151335	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12459567	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12460555	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12460615	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12977474	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12985477	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16974196	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs1962639	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1991460	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2304186	0.91[ASW][hapmap];0.89[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes]
rs2368575	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs33933140	0.83[ASW][hapmap];0.89[CEU][hapmap];0.86[CHB][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34894858	0.82[CHB][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap]
rs35562135	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3745195	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3746006	0.81[JPT][hapmap]
rs4479364	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4490097	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4502340	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]
rs4524046	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802072	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4802076	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs4803324	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4803325	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4803326	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803327	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55710016	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57158010	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58502633	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59263025	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7259273	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7259541	0.85[JPT][hapmap]
rs73046335	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7507651	0.81[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7508513	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8110323	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs892117	0.82[CHB][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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	esv3386713	chr19:40794161-40828617	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs890773	MIA	cis	lymphoblastoid	seeQTL
rs890773	PLAUR	cis	cerebellum	SCAN
rs890773	VASP	cis	cerebellum	SCAN
rs890773	ERCC1	cis	parietal	SCAN
rs890773	DMRTC2	cis	parietal	SCAN
rs890773	TMEM91	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40792000-40826200	Weak transcription	Hela-S3	cervix
2	chr19:40800400-40826400	Weak transcription	Brain Angular Gyrus	brain
3	chr19:40802800-40828000	Weak transcription	NH-A	brain
4	chr19:40810600-40829800	Weak transcription	NHDF-Ad	bronchial
5	chr19:40810800-40826200	Weak transcription	HMEC	breast
6	chr19:40811400-40826600	Weak transcription	NHEK	skin
7	chr19:40811600-40826600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr19:40811800-40826400	Weak transcription	Brain Substantia Nigra	brain
9	chr19:40811800-40826600	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr19:40811800-40826600	Weak transcription	Fetal Lung	lung
11	chr19:40811800-40831600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr19:40815400-40832800	Weak transcription	Fetal Brain Male	brain
13	chr19:40817400-40827400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr19:40817600-40827200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr19:40819200-40826800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr19:40819200-40834000	Weak transcription	Fetal Kidney	kidney
17	chr19:40819400-40828200	Weak transcription	Osteobl	bone
18	chr19:40819800-40826600	Weak transcription	Primary B cells from cord blood	blood
19	chr19:40819800-40826800	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr19:40820000-40827400	Weak transcription	HepG2	liver
21	chr19:40820200-40826400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr19:40820600-40826600	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr19:40820600-40827400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr19:40820800-40826600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr19:40820800-40848400	Strong transcription	Dnd41	blood
26	chr19:40821200-40831800	Weak transcription	K562	blood
27	chr19:40821400-40827200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr19:40821400-40827800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr19:40821400-40835000	Strong transcription	Fetal Intestine Small	intestine
30	chr19:40821400-40846000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr19:40821800-40826600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr19:40821800-40829000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr19:40822000-40829200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr19:40822000-40833400	Weak transcription	Fetal Heart	heart
35	chr19:40822000-40842400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr19:40822000-40843400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr19:40822000-40851000	Strong transcription	Fetal Stomach	stomach
38	chr19:40822200-40826400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr19:40822200-40828000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr19:40822200-40828600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr19:40822200-40842400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr19:40822200-40842600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr19:40822200-40843200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr19:40822200-40845400	Strong transcription	Fetal Muscle Leg	muscle
45	chr19:40822400-40826400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr19:40822400-40846200	Strong transcription	Fetal Muscle Trunk	muscle
47	chr19:40822600-40826400	Weak transcription	Primary T cells from cord blood	blood
48	chr19:40822600-40826600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr19:40822600-40826800	Weak transcription	Colon Smooth Muscle	Colon
50	chr19:40822600-40828200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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