Variant report

Variant	rs2607424
Chromosome Location	chr19:41275147-41275148
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA2	chr19:41274894-41275222	HepG2	liver:	n/a	n/a
2	FOXA1	chr19:41274858-41275205	HepG2	liver:	n/a	n/a
3	POLR2A	chr19:41274413-41275360	SK-N-MC	brain:	n/a	n/a
4	FOXA1	chr19:41274868-41275216	HepG2	liver:	n/a	n/a
5	ARID3A	chr19:41274915-41275263	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:41256102..41258357-chr19:41273120..41276107,2	MCF-7	breast:
2	chr19:41274845..41276848-chr19:41281762..41284893,3	K562	blood:
3	chr19:41274845..41278396-chr19:41279079..41284996,6	K562	blood:
4	chr19:41273890..41276228-chr19:41304593..41306806,2	MCF-7	breast:
5	chr19:41274913..41277025-chr19:41302657..41305848,3	K562	blood:
6	chr19:41267917..41272263-chr19:41274538..41279747,5	K562	blood:

No data

Variant related genes	Relation type
MIA	TF binding region
MIA-RAB4B	TF binding region
ENSG00000188493	Chromatin interaction
ENSG00000261857	Chromatin interaction
ENSG00000269858	Chromatin interaction
ENSG00000167578	Chromatin interaction
ENSG00000171570	Chromatin interaction
ENSG00000077312	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs2249835	1.00[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];0.98[MKK][hapmap];0.92[TSI][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2545755	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2545774	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2604869	1.00[ASW][hapmap];0.95[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];0.91[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2604893	0.90[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2604895	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2607414	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2607415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2644898	0.91[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2644916	0.86[CEU][hapmap];0.90[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4803368	0.90[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7249450	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2607424	NKPD1	cis	cerebellum	SCAN
rs2607424	LMTK3	cis	parietal	SCAN
rs2607424	LIN7B	cis	parietal	SCAN
rs2607424	C19orf54	cis	lymphoblastoid	seeQTL
rs2607424	FLJ41131	cis	multi-tissue	Pritchard
rs2607424	C19orf54	cis	Lymphoblastoid	GTEx
rs2607424	TULP2	cis	cerebellum	SCAN
rs2607424	KCNN4	cis	cerebellum	SCAN

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	chr19:41261600-41275200	Strong transcription	Fetal Muscle Trunk	muscle
6	chr19:41261800-41276800	Strong transcription	Fetal Intestine Small	intestine
7	chr19:41261800-41278200	Strong transcription	Fetal Stomach	stomach
8	chr19:41261800-41282800	Weak transcription	Right Atrium	heart
9	chr19:41262000-41276200	Strong transcription	Thymus	Thymus
10	chr19:41262800-41275200	Strong transcription	Liver	Liver
11	chr19:41263400-41275200	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr19:41264600-41278000	Strong transcription	A549	lung
13	chr19:41270400-41282600	Weak transcription	Fetal Brain Male	brain
14	chr19:41271800-41275200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr19:41271800-41276800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr19:41271800-41279800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr19:41271800-41279800	Weak transcription	HMEC	breast
18	chr19:41271800-41282600	Weak transcription	Fetal Kidney	kidney
19	chr19:41271800-41282600	Weak transcription	HSMM	muscle
20	chr19:41271800-41283000	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr19:41272000-41276800	Weak transcription	Primary T cells from cord blood	blood
22	chr19:41272000-41279400	Weak transcription	Ovary	ovary
23	chr19:41272000-41280400	Weak transcription	NHEK	skin
24	chr19:41272000-41280600	Weak transcription	NH-A	brain
25	chr19:41272000-41281200	Weak transcription	Osteobl	bone
26	chr19:41272000-41282600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr19:41272000-41282600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr19:41272000-41282600	Weak transcription	Brain Angular Gyrus	brain
29	chr19:41272000-41282600	Weak transcription	HUVEC	blood vessel
30	chr19:41272000-41282800	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr19:41272000-41282800	Weak transcription	Psoas Muscle	Psoas
32	chr19:41272000-41282800	Weak transcription	Small Intestine	intestine
33	chr19:41272000-41282800	Weak transcription	NHDF-Ad	bronchial
34	chr19:41272200-41275600	Strong transcription	Placenta	Placenta
35	chr19:41272200-41276800	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr19:41272200-41276800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr19:41272200-41277000	Weak transcription	Primary hematopoietic stem cells	blood
38	chr19:41272200-41277000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr19:41272200-41280800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr19:41272200-41280800	Weak transcription	Stomach Mucosa	stomach
41	chr19:41272200-41281200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr19:41272200-41281200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr19:41272200-41281200	Weak transcription	K562	blood
44	chr19:41272200-41282600	Weak transcription	Fetal Lung	lung
45	chr19:41272200-41282600	Weak transcription	Stomach Smooth Muscle	stomach
46	chr19:41272200-41282600	Weak transcription	Dnd41	blood
47	chr19:41272200-41282600	Weak transcription	HSMMtube	muscle
48	chr19:41272200-41282600	Weak transcription	NHLF	lung
49	chr19:41272200-41282800	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr19:41272200-41282800	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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