Variant report

Variant	rs332849
Chromosome Location	chr19:38643951-38643952
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38642798..38644805-chr19:38646694..38649003,2	K562	blood:
2	chr19:38635598..38638307-chr19:38643288..38645497,2	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10404957	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1654366	0.80[CHB][hapmap];0.82[CHD][hapmap]
rs1654369	0.83[ASN][1000 genomes]
rs1725472	0.80[CHB][hapmap];0.82[CHD][hapmap]
rs1725489	0.93[CHD][hapmap];0.88[JPT][hapmap]
rs2005055	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2099340	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2278429	0.84[CEU][hapmap]
rs2384778	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2569412	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs332843	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs332844	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs332848	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs332850	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs332851	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs332855	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs332856	1.00[CEU][hapmap];0.82[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs332858	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs332864	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35932728	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4802251	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6508765	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs705507	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8100128	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8100144	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8101826	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8109695	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8109799	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8111180	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8112798	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs855614	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs855632	0.92[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9941474	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv833821	chr19:38629937-38756792	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs332849	ZNF780A	cis	cerebellum	SCAN
rs332849	IRGC	cis	parietal	SCAN
rs332849	PAPL	cis	cerebellum	SCAN
rs332849	LYPD3	cis	parietal	SCAN
rs332849	CIC	cis	cerebellum	SCAN
rs332849	CCDC61	cis	parietal	SCAN
rs332849	IGFL1	cis	cerebellum	SCAN
rs332849	EGLN2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38600600-38652800	Weak transcription	NHDF-Ad	bronchial
2	chr19:38611000-38652800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr19:38611600-38653000	Weak transcription	HUVEC	blood vessel
4	chr19:38611800-38653000	Weak transcription	Fetal Kidney	kidney
5	chr19:38613800-38652200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr19:38613800-38652600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr19:38616000-38652600	Strong transcription	Primary B cells from peripheral blood	blood
8	chr19:38617000-38652000	Strong transcription	Fetal Intestine Small	intestine
9	chr19:38618200-38651000	Strong transcription	Fetal Intestine Large	intestine
10	chr19:38619600-38647800	Strong transcription	Fetal Stomach	stomach
11	chr19:38624400-38652400	Weak transcription	Fetal Thymus	thymus
12	chr19:38626400-38652200	Strong transcription	A549	lung
13	chr19:38626800-38646000	Weak transcription	HMEC	breast
14	chr19:38627000-38652400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr19:38628400-38652600	Weak transcription	Right Atrium	heart
16	chr19:38628600-38645000	Strong transcription	Sigmoid Colon	Sigmoid Colon
17	chr19:38628800-38645200	Strong transcription	Duodenum Mucosa	Duodenum
18	chr19:38628800-38646400	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr19:38628800-38651200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr19:38629200-38652600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr19:38629600-38651600	Strong transcription	GM12878-XiMat	blood
22	chr19:38633000-38651000	Strong transcription	Primary B cells from cord blood	blood
23	chr19:38633000-38652400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr19:38633200-38652800	Weak transcription	Colon Smooth Muscle	Colon
25	chr19:38633400-38650800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr19:38633400-38653000	Weak transcription	Fetal Brain Male	brain
27	chr19:38635400-38652600	Weak transcription	Stomach Mucosa	stomach
28	chr19:38636600-38652600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr19:38637000-38652400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr19:38637000-38652800	Weak transcription	Brain Substantia Nigra	brain
31	chr19:38638200-38667200	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr19:38638400-38645000	Strong transcription	Gastric	stomach
33	chr19:38638400-38650600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr19:38639400-38646600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr19:38639600-38644600	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr19:38640000-38647000	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr19:38640200-38645000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr19:38640200-38645000	Strong transcription	Primary hematopoietic stem cells	blood
39	chr19:38640200-38645000	Strong transcription	Colonic Mucosa	Colon
40	chr19:38640200-38645000	Strong transcription	Pancreas	Pancrea
41	chr19:38640400-38644800	Strong transcription	Fetal Muscle Trunk	muscle
42	chr19:38640400-38645000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr19:38640400-38645000	Strong transcription	Adipose Nuclei	Adipose
44	chr19:38640400-38646400	Strong transcription	Primary T cells from cord blood	blood
45	chr19:38640600-38646600	Strong transcription	Fetal Muscle Leg	muscle
46	chr19:38641400-38645000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr19:38641600-38644800	Strong transcription	H9 Cell Line	embryonic stem cell
48	chr19:38641600-38645000	Strong transcription	Stomach Smooth Muscle	stomach
49	chr19:38641600-38645200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr19:38641600-38645200	Strong transcription	Lung	lung

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