Variant report

Variant	rs7249956
Chromosome Location	chr19:18715203-18715204
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTBP2	chr19:18714944-18715742	H1-hESC	embryonic stem cell:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:18713204..18718867-chr19:18719015..18725496,7	MCF-7	breast:
2	chr19:18714829..18718349-chr19:18723409..18727026,4	K562	blood:
3	chr19:18713933..18717054-chr19:18723624..18727026,3	K562	blood:
4	chr19:18714423..18716001-chr19:18720923..18723094,2	K562	blood:
5	chr19:18713980..18716446-chr19:18757354..18760125,2	K562	blood:
6	chr19:18714258..18716711-chr19:18719461..18722423,3	K562	blood:

No data

Variant related genes	Relation type
TMEM59L	TF binding region
ENSG00000105696	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs11668617	0.91[CHD][hapmap];0.82[JPT][hapmap]
rs12461284	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2002632	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2074177	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2238647	0.95[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2283617	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.87[JPT][hapmap];0.83[MEX][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2314662	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3761031	0.84[ASN][1000 genomes]
rs4808140	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4808141	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4808822	0.85[CEU][hapmap]
rs4808828	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7246833	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7252535	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7253677	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8109611	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8110573	0.86[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs886243	0.82[AMR][1000 genomes]
rs889363	0.86[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 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	nsv911281	chr19:18613917-18758255	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	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
6	nsv833776	chr19:18638028-18782264	Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
7	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
8	nsv911287	chr19:18699333-18727913	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
9	nsv911288	chr19:18700047-18739497	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
10	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
11	nsv911290	chr19:18701499-18720981	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
12	nsv911291	chr19:18701499-18726856	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
13	nsv911292	chr19:18701499-18731658	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
14	esv1822476	chr19:18710535-18717425	Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7249956	ISYNA1	cis	parietal	SCAN
rs7249956	ZNF682	cis	parietal	SCAN
rs7249956	INSL3	cis	cerebellum	SCAN
rs7249956	GMIP	cis	parietal	SCAN
rs7249956	CRLF1	cis	Muscle Skeletal	GTEx
rs7249956	UBA52	cis	lymphoblastoid	seeQTL

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18706400-18716200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr19:18713000-18716200	Weak transcription	Pancreas	Pancrea
3	chr19:18713600-18716800	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr19:18714000-18715400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
5	chr19:18714000-18718200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr19:18714200-18715400	Flanking Active TSS	HSMM	muscle
7	chr19:18714200-18715600	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:18714200-18716600	Bivalent Enhancer	Fetal Stomach	stomach
9	chr19:18714200-18717200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr19:18714400-18715600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
11	chr19:18714400-18715800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
12	chr19:18714400-18716200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
13	chr19:18714400-18716400	Weak transcription	A549	lung
14	chr19:18714400-18716600	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
15	chr19:18714400-18716800	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr19:18714400-18717600	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
17	chr19:18714400-18718400	Active TSS	HSMMtube	muscle
18	chr19:18714400-18719000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr19:18714600-18715800	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr19:18714600-18716200	Active TSS	Right Atrium	heart
21	chr19:18714600-18716400	Bivalent Enhancer	Fetal Muscle Leg	muscle
22	chr19:18714800-18716200	Flanking Active TSS	HepG2	liver
23	chr19:18714800-18716800	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr19:18715000-18715400	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr19:18715000-18715400	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr19:18715000-18715400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
27	chr19:18715000-18715400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
28	chr19:18715000-18715400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr19:18715000-18715600	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
30	chr19:18715000-18716000	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr19:18715000-18716000	Active TSS	Right Ventricle	heart
32	chr19:18715000-18716400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr19:18715000-18716400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
34	chr19:18715000-18717000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
35	chr19:18715000-18718200	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
36	chr19:18715200-18715400	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
37	chr19:18715200-18715400	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
38	chr19:18715200-18715400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
39	chr19:18715200-18715400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr19:18715200-18715400	Bivalent Enhancer	Brain Anterior Caudate	brain
41	chr19:18715200-18715400	Bivalent Enhancer	Brain Cingulate Gyrus	brain
42	chr19:18715200-18715400	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
43	chr19:18715200-18715600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
44	chr19:18715200-18715600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
45	chr19:18715200-18716200	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell

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