Variant report

Variant	rs304719
Chromosome Location	chr19:44108635-44108636
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:44105666..44109399-chr19:44121081..44124426,3	K562	blood:
2	chr19:44099425..44103401-chr19:44107889..44111308,5	MCF-7	breast:
3	chr19:44108130..44109917-chr19:44159036..44160789,2	MCF-7	breast:
4	chr19:44108093..44109793-chr19:44111423..44113227,2	MCF-7	breast:
5	chr19:44106723..44108884-chr19:44122339..44124163,2	MCF-7	breast:
6	chr19:44101681..44103493-chr19:44106654..44108776,2	K562	blood:
7	chr19:44106374..44108896-chr19:44122542..44124063,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000131116	Chromatin interaction
ENSG00000124444	Chromatin interaction
ENSG00000167378	Chromatin interaction
ENSG00000011422	Chromatin interaction
ENSG00000226763	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10402946	0.85[ASW][hapmap];0.97[LWK][hapmap];0.83[YRI][hapmap]
rs17655646	0.86[CEU][hapmap]
rs2240633	1.00[CEU][hapmap];0.98[GIH][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2270075	0.87[AFR][1000 genomes]
rs304720	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs304722	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs304723	0.93[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];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs304726	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3213282	0.82[ASN][1000 genomes]
rs34521657	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34637472	0.93[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35346236	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs365063	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3803910	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs427115	0.85[ASW][hapmap];1.00[CEU][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4803646	0.82[CEU][hapmap]
rs4803647	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7245651	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8101956	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][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	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv833839	chr19:44099813-44272299	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs304719	ELSPBP1	cis	cerebellum	SCAN
rs304719	STRN4	cis	cerebellum	SCAN
rs304719	PRRG2	cis	cerebellum	SCAN
rs304719	IZUMO2	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44101600-44112000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:44101800-44109400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:44101800-44111600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr19:44101800-44123200	Weak transcription	Small Intestine	intestine
5	chr19:44102000-44122600	Weak transcription	Fetal Kidney	kidney
6	chr19:44102200-44111000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr19:44102200-44111200	Strong transcription	Fetal Muscle Leg	muscle
8	chr19:44102200-44113600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr19:44102200-44114200	Weak transcription	NH-A	brain
10	chr19:44102200-44114600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr19:44102200-44122600	Weak transcription	Psoas Muscle	Psoas
12	chr19:44102400-44109600	Weak transcription	Fetal Brain Male	brain
13	chr19:44102400-44110800	Weak transcription	Colon Smooth Muscle	Colon
14	chr19:44102400-44119600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr19:44102400-44122600	Weak transcription	NHDF-Ad	bronchial
16	chr19:44102600-44109800	Strong transcription	Fetal Muscle Trunk	muscle
17	chr19:44102600-44115800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr19:44102600-44116200	Weak transcription	Hela-S3	cervix
19	chr19:44102600-44120600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr19:44102600-44121200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr19:44102600-44122600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr19:44102600-44122600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr19:44102800-44120000	Strong transcription	Fetal Stomach	stomach
24	chr19:44103000-44111200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr19:44103200-44115000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr19:44103400-44109800	Weak transcription	HMEC	breast
27	chr19:44104000-44111000	Weak transcription	HUVEC	blood vessel
28	chr19:44104000-44111800	Weak transcription	Aorta	Aorta
29	chr19:44104000-44114000	Weak transcription	NHLF	lung
30	chr19:44104000-44116000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr19:44104000-44116200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr19:44104400-44110200	Weak transcription	Brain Substantia Nigra	brain
33	chr19:44104400-44110600	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr19:44104400-44122800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr19:44104600-44110000	Weak transcription	NHEK	skin
36	chr19:44104600-44110400	Weak transcription	Pancreas	Pancrea
37	chr19:44104600-44110600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr19:44104600-44111000	Weak transcription	Osteobl	bone
39	chr19:44104600-44111600	Weak transcription	Colonic Mucosa	Colon
40	chr19:44104600-44111800	Weak transcription	Esophagus	oesophagus
41	chr19:44104600-44115800	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr19:44104600-44116200	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr19:44104600-44116400	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr19:44104800-44111000	Weak transcription	Right Ventricle	heart
45	chr19:44104800-44111000	Weak transcription	HepG2	liver
46	chr19:44104800-44123000	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr19:44105200-44115800	Weak transcription	HSMM	muscle
48	chr19:44105600-44111000	Weak transcription	Primary hematopoietic stem cells	blood
49	chr19:44105600-44112200	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr19:44105800-44110200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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