Variant report

Variant	rs7248428
Chromosome Location	chr19:38638423-38638424
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	chr19:38633263..38636587-chr19:38638025..38640526,3	K562	blood:
2	chr19:38633389..38636227-chr19:38637615..38640869,3	K562	blood:

Extended variants
information (count: 94 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10401165	0.85[ASN][1000 genomes]
rs10403716	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10405667	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10412762	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10412865	0.97[ASN][1000 genomes]
rs10413751	0.81[JPT][hapmap]
rs10420506	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10422665	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1568975	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1614979	0.87[CEU][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1622409	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1625884	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1654349	0.81[JPT][hapmap]
rs1654355	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1654357	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1654358	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1654359	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1654365	0.87[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1654367	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1725461	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1725473	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1725475	0.81[JPT][hapmap]
rs1725479	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1725512	0.81[CEU][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2005054	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2010234	0.84[YRI][hapmap]
rs2082442	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2082443	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28412601	0.83[AMR][1000 genomes]
rs28495744	0.82[ASN][1000 genomes]
rs28581256	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3760882	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3810356	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4802233	0.81[CEU][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4802239	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4802247	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4802256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4802278	0.80[CEU][hapmap];0.90[CHB][hapmap]
rs4803786	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4803800	0.92[EUR][1000 genomes]
rs4803801	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4803802	0.92[EUR][1000 genomes]
rs4803803	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4803809	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4803810	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4803828	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4803829	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4803862	0.80[CEU][hapmap];0.90[CHB][hapmap]
rs56166457	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs58152231	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs59185302	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59579475	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59924887	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61388128	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6508767	0.85[ASN][1000 genomes]
rs705505	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71179415	0.83[EUR][1000 genomes]
rs7245788	0.90[ASN][1000 genomes]
rs7250034	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7256332	0.82[ASN][1000 genomes]
rs729625	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs729626	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs735615	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73627654	0.90[ASN][1000 genomes]
rs73627663	0.90[ASN][1000 genomes]
rs73627676	0.90[ASN][1000 genomes]
rs73627686	0.80[ASN][1000 genomes]
rs754123	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8105468	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8106266	0.89[EUR][1000 genomes]
rs855601	0.81[JPT][hapmap]
rs855603	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs855619	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs855621	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs855623	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs855624	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs855625	0.83[EUR][1000 genomes]
rs855627	0.86[EUR][1000 genomes]
rs855630	0.81[EUR][1000 genomes]
rs855633	0.87[CEU][hapmap];0.91[CHB][hapmap];0.85[EUR][1000 genomes]
rs855634	0.85[EUR][1000 genomes]
rs855636	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs855637	0.81[JPT][hapmap]
rs855638	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs855640	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs855641	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs860623	0.93[CEU][hapmap];0.90[CHB][hapmap];0.85[EUR][1000 genomes]
rs863020	0.93[CEU][hapmap];0.90[CHB][hapmap];0.86[EUR][1000 genomes]
rs941039	0.93[CEU][hapmap];0.90[CHB][hapmap];0.85[EUR][1000 genomes]
rs941040	0.81[CEU][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9941456	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9941467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7248428	SIPA1L3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38591800-38642800	Weak transcription	Small Intestine	intestine
2	chr19:38600600-38652800	Weak transcription	NHDF-Ad	bronchial
3	chr19:38610800-38643600	Weak transcription	HepG2	liver
4	chr19:38611000-38652800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr19:38611600-38641400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr19:38611600-38653000	Weak transcription	HUVEC	blood vessel
7	chr19:38611800-38642600	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr19:38611800-38653000	Weak transcription	Fetal Kidney	kidney
9	chr19:38613800-38639000	Weak transcription	Left Ventricle	heart
10	chr19:38613800-38641800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr19:38613800-38643200	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr19:38613800-38652200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr19:38613800-38652600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr19:38616000-38652600	Strong transcription	Primary B cells from peripheral blood	blood
15	chr19:38616200-38641600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr19:38616600-38642000	Weak transcription	Dnd41	blood
17	chr19:38617000-38652000	Strong transcription	Fetal Intestine Small	intestine
18	chr19:38618200-38651000	Strong transcription	Fetal Intestine Large	intestine
19	chr19:38619600-38647800	Strong transcription	Fetal Stomach	stomach
20	chr19:38621600-38642800	Weak transcription	NHLF	lung
21	chr19:38622600-38641800	Weak transcription	Aorta	Aorta
22	chr19:38623000-38642800	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr19:38624400-38652400	Weak transcription	Fetal Thymus	thymus
24	chr19:38626000-38643400	Weak transcription	Placenta	Placenta
25	chr19:38626400-38642000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr19:38626400-38643400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr19:38626400-38652200	Strong transcription	A549	lung
28	chr19:38626600-38641000	Weak transcription	Hela-S3	cervix
29	chr19:38626600-38643600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:38626800-38646000	Weak transcription	HMEC	breast
31	chr19:38627000-38652400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr19:38627600-38642800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr19:38628400-38652600	Weak transcription	Right Atrium	heart
34	chr19:38628600-38645000	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr19:38628800-38645200	Strong transcription	Duodenum Mucosa	Duodenum
36	chr19:38628800-38646400	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr19:38628800-38651200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr19:38629200-38652600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr19:38629600-38651600	Strong transcription	GM12878-XiMat	blood
40	chr19:38633000-38651000	Strong transcription	Primary B cells from cord blood	blood
41	chr19:38633000-38652400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr19:38633200-38652800	Weak transcription	Colon Smooth Muscle	Colon
43	chr19:38633400-38638600	Strong transcription	HSMM	muscle
44	chr19:38633400-38650800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr19:38633400-38653000	Weak transcription	Fetal Brain Male	brain
46	chr19:38633600-38640000	Weak transcription	K562	blood
47	chr19:38634000-38639400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr19:38634200-38642000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr19:38634200-38642200	Weak transcription	Ovary	ovary
50	chr19:38634200-38643200	Weak transcription	Fetal Lung	lung

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