Variant report

Variant	rs7246437
Chromosome Location	chr19:18786784-18786785
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:18561437..18562386-chr19:18786264..18787156,2	MCF-7	breast:
2	chr19:18785757..18787388-chr19:18793270..18795372,2	MCF-7	breast:
3	chr19:18786344..18788894-chr19:18792573..18794352,2	K562	blood:
4	chr19:18784039..18786803-chr19:18794449..18796829,2	K562	blood:
5	chr19:18682620..18684226-chr19:18786730..18789079,2	MCF-7	breast:
6	chr14:65768227..65770928-chr19:18785251..18788055,2	MCF-7	breast:
7	chr19:18703804..18708043-chr19:18784687..18787228,3	K562	blood:
8	chr19:18698316..18700279-chr19:18785499..18787452,2	MCF-7	breast:
9	chr19:18781390..18783867-chr19:18783988..18789720,5	K562	blood:
10	chr19:18786668..18789315-chr19:18956756..18958447,2	MCF-7	breast:
11	chr19:18580151..18581282-chr19:18786328..18787235,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000006016	Chromatin interaction
ENSG00000105662	Chromatin interaction
ENSG00000006015	Chromatin interaction
ENSG00000221983	Chromatin interaction
ENSG00000258760	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10221489	0.81[CHB][hapmap]
rs10412053	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10412858	1.00[ASW][hapmap];0.88[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.84[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10419226	0.89[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.94[ASN][1000 genomes]
rs10420228	0.94[ASN][1000 genomes]
rs10421503	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10423674	0.81[CHB][hapmap]
rs10854003	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11085236	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11883401	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12976113	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1473116	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.98[ASN][1000 genomes]
rs1991017	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs2214524	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2385178	0.92[ASN][1000 genomes]
rs2891698	0.82[ASN][1000 genomes]
rs3829671	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4808145	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4808147	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6510995	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6510996	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7257812	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs757347	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs757350	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8100824	0.89[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8102046	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs876982	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs886443	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs889364	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv532615	chr19:18534867-18796031	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	nsv911282	chr19:18624964-18928480	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv911286	chr19:18652844-18811112	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
6	nsv911289	chr19:18700047-18811112	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7246437	GDF1	cis	parietal	SCAN
rs7246437	UBA52	cis	lymphoblastoid	seeQTL
rs7246437	CRLF1	cis	cerebellum	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18760400-18794800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr19:18770400-18793600	Weak transcription	GM12878-XiMat	blood
3	chr19:18771800-18788200	Weak transcription	K562	blood
4	chr19:18773200-18788000	Weak transcription	NHEK	skin
5	chr19:18774600-18787400	Weak transcription	Hela-S3	cervix
6	chr19:18774800-18788000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr19:18775200-18793800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:18777800-18793800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr19:18780000-18788200	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr19:18780000-18788800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr19:18780200-18786800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr19:18780200-18788000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr19:18780200-18788000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr19:18780200-18788800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr19:18780200-18793400	Weak transcription	Primary hematopoietic stem cells	blood
16	chr19:18780200-18793800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr19:18780400-18788000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr19:18780400-18788000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr19:18780400-18793800	Weak transcription	Right Ventricle	heart
20	chr19:18780600-18788000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr19:18780600-18788200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr19:18780600-18788800	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr19:18780800-18793800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr19:18780800-18793800	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr19:18781000-18787200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr19:18781000-18788000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr19:18781000-18789000	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr19:18781000-18793800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr19:18781200-18788000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr19:18781200-18788600	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr19:18781200-18789000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr19:18781200-18789000	Weak transcription	Liver	Liver
33	chr19:18781400-18787200	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr19:18781400-18788000	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr19:18782000-18789600	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr19:18782200-18787400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr19:18782200-18793600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr19:18782800-18787600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr19:18782800-18793800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr19:18783000-18788200	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr19:18783000-18788200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr19:18783000-18788800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr19:18783200-18789200	Weak transcription	Psoas Muscle	Psoas
44	chr19:18783200-18793800	Weak transcription	Spleen	Spleen
45	chr19:18783400-18788200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr19:18783400-18793000	Weak transcription	Dnd41	blood
47	chr19:18783400-18793600	Weak transcription	Primary T cells from cord blood	blood
48	chr19:18783400-18793600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr19:18783600-18787800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr19:18783600-18788200	Weak transcription	Osteobl	bone

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