Variant report

Variant	rs2023878
Chromosome Location	chr19:18834124-18834125
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10221489	0.89[JPT][hapmap]
rs10423674	0.80[CHD][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs11085240	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11085241	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11668545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11668587	0.81[ASN][1000 genomes]
rs11878358	0.85[GIH][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs11880800	0.90[CEU][hapmap];0.95[EUR][1000 genomes]
rs12460629	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12462498	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12610715	0.85[GIH][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs2003475	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2240012	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs34482977	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60021783	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs757317	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8113096	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv911282	chr19:18624964-18928480	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv960927	chr19:18808010-18837082	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2023878	ANKLE1	cis	parietal	SCAN
rs2023878	CRTC1	cis	cerebellum	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18812000-18844200	Weak transcription	Fetal Kidney	kidney
2	chr19:18818000-18836600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr19:18819000-18844000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr19:18820400-18837000	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr19:18820400-18847200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr19:18820600-18846600	Weak transcription	Esophagus	oesophagus
7	chr19:18821200-18834400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr19:18821200-18844000	Weak transcription	Colonic Mucosa	Colon
9	chr19:18821200-18860600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr19:18821200-18861000	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr19:18821200-18864800	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr19:18822400-18835600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr19:18822600-18836400	Weak transcription	Adipose Nuclei	Adipose
14	chr19:18822600-18843800	Weak transcription	Colon Smooth Muscle	Colon
15	chr19:18822600-18844000	Weak transcription	NHLF	lung
16	chr19:18822800-18836800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr19:18824200-18846600	Weak transcription	Pancreas	Pancrea
18	chr19:18824600-18840600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr19:18824600-18843000	Weak transcription	Fetal Lung	lung
20	chr19:18824600-18847800	Weak transcription	Liver	Liver
21	chr19:18825000-18834600	Weak transcription	Fetal Brain Female	brain
22	chr19:18825000-18844000	Weak transcription	Right Atrium	heart
23	chr19:18825000-18845600	Weak transcription	Primary B cells from cord blood	blood
24	chr19:18826400-18840800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr19:18826600-18836200	Weak transcription	Ovary	ovary
26	chr19:18826800-18835000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr19:18827000-18846200	Weak transcription	Thymus	Thymus
28	chr19:18827600-18860600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr19:18828000-18841200	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr19:18828000-18841400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr19:18828200-18845600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr19:18828400-18834600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr19:18828400-18840600	Weak transcription	Gastric	stomach
34	chr19:18828400-18841400	Weak transcription	Spleen	Spleen
35	chr19:18828800-18850400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr19:18829000-18835600	Weak transcription	HepG2	liver
37	chr19:18829000-18842200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr19:18829000-18843800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr19:18829200-18835400	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr19:18829200-18842000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr19:18829200-18860000	Weak transcription	Primary monocytes fromperipheralblood	blood
42	chr19:18829200-18861400	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr19:18829400-18841000	Strong transcription	Fetal Intestine Small	intestine
44	chr19:18829400-18841400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr19:18829400-18842000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr19:18830200-18834600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr19:18830200-18836000	Weak transcription	Brain Angular Gyrus	brain
48	chr19:18830400-18845600	Weak transcription	Brain Hippocampus Middle	brain
49	chr19:18830400-18845800	Weak transcription	Brain Cingulate Gyrus	brain
50	chr19:18830600-18834200	Weak transcription	Brain Anterior Caudate	brain

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