Variant report

Variant	rs2607426
Chromosome Location	chr19:41274713-41274714
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:41274645-41274856	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr19:41271325-41274974	HepG2	liver:	n/a	n/a
3	POLR2A	chr19:41274413-41275360	SK-N-MC	brain:	n/a	n/a
4	RUNX3	chr19:41274636-41275006	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:41256102..41258357-chr19:41273120..41276107,2	MCF-7	breast:
2	chr19:41270648..41272782-chr19:41273219..41274815,2	MCF-7	breast:
3	chr19:41273890..41276228-chr19:41304593..41306806,2	MCF-7	breast:
4	chr19:41267917..41272263-chr19:41274538..41279747,5	K562	blood:

Variant related genes	Relation type
MIA	TF binding region
MIA-RAB4B	TF binding region
ENSG00000077312	Chromatin interaction
ENSG00000188493	Chromatin interaction
ENSG00000269858	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10420651	0.92[CHB][hapmap]
rs10420685	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs13108	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[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1455434	0.85[CHB][hapmap]
rs17726258	0.92[CHB][hapmap];0.83[CHD][hapmap];0.87[JPT][hapmap];0.83[TSI][hapmap];0.87[ASN][1000 genomes]
rs1869710	0.85[CHB][hapmap]
rs2230694	0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2233153	0.88[ASN][1000 genomes]
rs2233154	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2233156	0.92[CHB][hapmap];0.83[CHD][hapmap];0.87[JPT][hapmap];0.85[TSI][hapmap];0.88[ASN][1000 genomes]
rs2233159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2249854	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[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2254326	0.92[CHB][hapmap];0.80[CHD][hapmap];0.85[TSI][hapmap]
rs2279699	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2303723	0.92[CHB][hapmap];0.83[CHD][hapmap]
rs2545760	0.91[ASN][1000 genomes]
rs2545763	0.87[JPT][hapmap]
rs2545772	0.81[JPT][hapmap]
rs2545777	0.99[ASN][1000 genomes]
rs2545778	0.99[ASN][1000 genomes]
rs2561531	0.85[CHB][hapmap]
rs2604866	0.87[JPT][hapmap]
rs2604876	1.00[ASN][1000 genomes]
rs2604877	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2604909	0.94[ASN][1000 genomes]
rs2604910	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2604911	0.94[ASN][1000 genomes]
rs2607411	0.98[ASN][1000 genomes]
rs2607412	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2607413	0.98[ASN][1000 genomes]
rs2607416	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2607418	0.92[CHB][hapmap];0.80[CHD][hapmap]
rs2607419	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2607421	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2607422	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2607423	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2607425	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2644917	0.97[ASN][1000 genomes]
rs34842744	0.94[ASN][1000 genomes]
rs56891752	0.99[ASN][1000 genomes]
rs60533951	0.95[ASN][1000 genomes]
rs8107978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8109099	0.99[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	esv1802033	chr19:41256131-41284240	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	40 gene(s)	inside rSNPs	diseases
2	esv1801805	chr19:41256581-41284363	Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	37 gene(s)	inside rSNPs	diseases
3	nsv833832	chr19:41260363-41334597	Strong transcription Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2607426	C19orf54	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41258000-41283000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:41259000-41275200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:41260600-41277200	Strong transcription	Fetal Brain Female	brain
4	chr19:41260800-41283200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr19:41261600-41275000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr19:41261600-41275200	Strong transcription	Fetal Muscle Trunk	muscle
7	chr19:41261800-41276800	Strong transcription	Fetal Intestine Small	intestine
8	chr19:41261800-41278200	Strong transcription	Fetal Stomach	stomach
9	chr19:41261800-41282800	Weak transcription	Right Atrium	heart
10	chr19:41262000-41276200	Strong transcription	Thymus	Thymus
11	chr19:41262800-41275200	Strong transcription	Liver	Liver
12	chr19:41263400-41275200	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr19:41264600-41278000	Strong transcription	A549	lung
14	chr19:41270400-41282600	Weak transcription	Fetal Brain Male	brain
15	chr19:41271800-41275200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr19:41271800-41276800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
17	chr19:41271800-41279800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr19:41271800-41279800	Weak transcription	HMEC	breast
19	chr19:41271800-41282600	Weak transcription	Fetal Kidney	kidney
20	chr19:41271800-41282600	Weak transcription	HSMM	muscle
21	chr19:41271800-41283000	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr19:41272000-41276800	Weak transcription	Primary T cells from cord blood	blood
23	chr19:41272000-41279400	Weak transcription	Ovary	ovary
24	chr19:41272000-41280400	Weak transcription	NHEK	skin
25	chr19:41272000-41280600	Weak transcription	NH-A	brain
26	chr19:41272000-41281200	Weak transcription	Osteobl	bone
27	chr19:41272000-41282600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr19:41272000-41282600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr19:41272000-41282600	Weak transcription	Brain Angular Gyrus	brain
30	chr19:41272000-41282600	Weak transcription	HUVEC	blood vessel
31	chr19:41272000-41282800	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr19:41272000-41282800	Weak transcription	Psoas Muscle	Psoas
33	chr19:41272000-41282800	Weak transcription	Small Intestine	intestine
34	chr19:41272000-41282800	Weak transcription	NHDF-Ad	bronchial
35	chr19:41272200-41274800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr19:41272200-41275600	Strong transcription	Placenta	Placenta
37	chr19:41272200-41276800	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr19:41272200-41276800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr19:41272200-41277000	Weak transcription	Primary hematopoietic stem cells	blood
40	chr19:41272200-41277000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
41	chr19:41272200-41280800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr19:41272200-41280800	Weak transcription	Stomach Mucosa	stomach
43	chr19:41272200-41281200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr19:41272200-41281200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr19:41272200-41281200	Weak transcription	K562	blood
46	chr19:41272200-41282600	Weak transcription	Fetal Lung	lung
47	chr19:41272200-41282600	Weak transcription	Stomach Smooth Muscle	stomach
48	chr19:41272200-41282600	Weak transcription	Dnd41	blood
49	chr19:41272200-41282600	Weak transcription	HSMMtube	muscle
50	chr19:41272200-41282600	Weak transcription	NHLF	lung

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