Variant report

Variant	rs7248570
Chromosome Location	chr19:41233298-41233299
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:41221116..41223827-chr19:41232060..41233716,2	MCF-7	breast:
2	chr19:41220005..41225073-chr19:41230462..41235365,8	K562	blood:
3	chr19:41231550..41234206-chr19:41242847..41245259,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123815	Chromatin interaction
ENSG00000086544	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10407351	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10425765	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11083566	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11548478	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12976551	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1469427	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1870086	0.82[ASW][hapmap];0.96[CEU][hapmap];0.80[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1870087	0.93[ASW][hapmap];1.00[CEU][hapmap];0.80[GIH][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap];0.88[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2115239	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2246095	0.91[JPT][hapmap]
rs2288451	0.85[CEU][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs2290692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2290693	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2369302	0.82[JPT][hapmap]
rs2604885	0.91[JPT][hapmap]
rs3745210	0.89[ASN][1000 genomes]
rs3745211	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3745216	0.85[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap];0.86[ASN][1000 genomes]
rs3865452	0.91[JPT][hapmap]
rs4802085	0.96[CEU][hapmap];0.91[JPT][hapmap];0.88[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4802086	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4802087	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4803360	0.85[EUR][1000 genomes]
rs7248468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7251246	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7257602	0.93[ASW][hapmap];0.92[CEU][hapmap];0.91[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7260405	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8111960	1.00[CEU][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs890934	0.87[ASW][hapmap];0.82[LWK][hapmap];0.82[YRI][hapmap]

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	esv1830682	chr19:40880127-41270055	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
2	esv1800615	chr19:41127465-41270055	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs7248570	LIN7B	cis	parietal	SCAN
rs7248570	ADCK4	cis	Nerve Tibial	GTEx
rs7248570	SYMPK	cis	cerebellum	SCAN
rs7248570	ZNF574	cis	parietal	SCAN
rs7248570	FOXA3	cis	parietal	SCAN
rs7248570	KCNN4	cis	cerebellum	SCAN
rs7248570	C19orf54	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:41225200-41235200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:41225200-41238800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:41225200-41243200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr19:41225800-41233400	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr19:41225800-41233400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr19:41225800-41236400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr19:41226400-41246200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr19:41226600-41238600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr19:41226600-41245600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:41226800-41236600	Weak transcription	GM12878-XiMat	blood
11	chr19:41226800-41245200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr19:41226800-41245600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr19:41226800-41245800	Strong transcription	Fetal Stomach	stomach
14	chr19:41227000-41254600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr19:41227200-41237000	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr19:41227200-41255200	Weak transcription	Fetal Heart	heart
17	chr19:41228000-41246800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr19:41228200-41238000	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr19:41228200-41241400	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr19:41228200-41246600	Strong transcription	Primary B cells from peripheral blood	blood
21	chr19:41228200-41246800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr19:41228400-41234000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr19:41228600-41233400	Weak transcription	Psoas Muscle	Psoas
24	chr19:41228600-41236000	Weak transcription	Fetal Brain Male	brain
25	chr19:41228600-41236400	Weak transcription	NHDF-Ad	bronchial
26	chr19:41228600-41237200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr19:41228600-41238800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr19:41228600-41240000	Weak transcription	Stomach Mucosa	stomach
29	chr19:41228600-41240400	Strong transcription	HepG2	liver
30	chr19:41228600-41241200	Strong transcription	A549	lung
31	chr19:41228600-41245400	Strong transcription	Fetal Muscle Trunk	muscle
32	chr19:41228600-41245600	Strong transcription	Fetal Muscle Leg	muscle
33	chr19:41228600-41250000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr19:41228600-41251000	Strong transcription	Fetal Brain Female	brain
35	chr19:41228800-41234200	Strong transcription	NHEK	skin
36	chr19:41229200-41240800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr19:41229200-41246800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr19:41229200-41247200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr19:41229400-41233800	Strong transcription	Gastric	stomach
40	chr19:41229400-41241200	Strong transcription	Duodenum Mucosa	Duodenum
41	chr19:41229400-41246800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr19:41229400-41246800	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr19:41229400-41249000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr19:41229600-41233400	Strong transcription	Brain Anterior Caudate	brain
45	chr19:41229600-41234600	Strong transcription	Osteobl	bone
46	chr19:41229600-41235200	Strong transcription	Primary hematopoietic stem cells	blood
47	chr19:41229600-41242000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr19:41229600-41244000	Strong transcription	Ovary	ovary
49	chr19:41229600-41245600	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr19:41229600-41246800	Strong transcription	Fetal Lung	lung

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