Variant report

Variant	rs7249622
Chromosome Location	chr19:38202001-38202002
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1060522	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10853710	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11083433	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.92[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11666172	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11668796	0.91[EUR][1000 genomes]
rs11671953	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11673497	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1291	0.92[YRI][hapmap]
rs16975299	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17246792	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28431170	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2891657	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34991303	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55871826	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55913702	0.91[EUR][1000 genomes]
rs55950325	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62108305	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62108351	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6508739	0.91[EUR][1000 genomes]
rs7253081	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7258385	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73037060	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv833820	chr19:38190721-38414049	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs7249622	POU2F2	cis	parietal	SCAN
rs7249622	ZNF573	cis	multi-tissue	Pritchard
rs7249622	PHLDB3	cis	cerebellum	SCAN
rs7249622	AC012309.5	cis	Thyroid	GTEx
rs7249622	IGFL3	cis	cerebellum	SCAN
rs7249622	PSG11	cis	cerebellum	SCAN
rs7249622	GSK3A	cis	parietal	SCAN
rs7249622	PHLDB3	cis	parietal	SCAN
rs7249622	SPTBN4	cis	cerebellum	SCAN

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38183200-38208800	Weak transcription	Fetal Heart	heart
2	chr19:38184400-38208800	Weak transcription	HepG2	liver
3	chr19:38187000-38207800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:38187000-38208000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:38187400-38205800	Strong transcription	Dnd41	blood
6	chr19:38187400-38208000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr19:38188200-38209200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr19:38189400-38209200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr19:38190000-38206600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr19:38190600-38209000	Weak transcription	Brain Substantia Nigra	brain
11	chr19:38190600-38209200	Weak transcription	HSMMtube	muscle
12	chr19:38190800-38202200	Weak transcription	NH-A	brain
13	chr19:38190800-38209000	Weak transcription	Stomach Mucosa	stomach
14	chr19:38190800-38209200	Weak transcription	Fetal Thymus	thymus
15	chr19:38190800-38209200	Weak transcription	Psoas Muscle	Psoas
16	chr19:38191200-38209200	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr19:38191200-38209200	Weak transcription	Colon Smooth Muscle	Colon
18	chr19:38192200-38203000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr19:38193800-38209000	Weak transcription	Hela-S3	cervix
20	chr19:38194000-38203000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr19:38194200-38202800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr19:38194600-38206600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr19:38195200-38204400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr19:38196000-38203000	ZNF genes & repeats	Liver	Liver
25	chr19:38196000-38204200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr19:38196200-38202200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr19:38196200-38202600	Strong transcription	Left Ventricle	heart
28	chr19:38196200-38204400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
29	chr19:38196600-38202200	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr19:38196600-38202200	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr19:38196600-38202400	Strong transcription	Stomach Smooth Muscle	stomach
32	chr19:38196800-38202800	Strong transcription	Fetal Muscle Trunk	muscle
33	chr19:38197000-38203000	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr19:38197000-38203000	Strong transcription	Brain Inferior Temporal Lobe	brain
35	chr19:38197200-38202800	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr19:38197200-38203000	Strong transcription	Fetal Muscle Leg	muscle
37	chr19:38197200-38203400	Strong transcription	Primary T cells from cord blood	blood
38	chr19:38197400-38202800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
39	chr19:38197600-38208800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr19:38198400-38202600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr19:38198400-38202600	Strong transcription	Muscle Satellite Cultured Cells	--
42	chr19:38198600-38204400	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
43	chr19:38198800-38202200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr19:38198800-38202200	Weak transcription	Aorta	Aorta
45	chr19:38198800-38203400	Strong transcription	Ovary	ovary
46	chr19:38198800-38208800	Weak transcription	Fetal Brain Male	brain
47	chr19:38198800-38209000	Weak transcription	Spleen	Spleen
48	chr19:38198800-38209200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr19:38198800-38209200	Weak transcription	Gastric	stomach
50	chr19:38198800-38209400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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