Variant report

Variant	rs3730050
Chromosome Location	chr19:40770982-40770983
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:40768260..40771807-chr19:40783478..40786593,4	K562	blood:
2	chr19:40770481..40772610-chr19:40774016..40777021,3	K562	blood:
3	chr19:40730135..40732831-chr19:40769478..40772203,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105219	Chromatin interaction
ENSG00000105221	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10402740	0.81[JPT][hapmap];0.87[MEX][hapmap]
rs10405207	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1129156	0.82[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap]
rs11668242	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11880261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12974529	0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12981110	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2304184	0.82[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];0.81[ASN][1000 genomes]
rs2304189	0.89[CHB][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs339526	0.90[CHB][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap]
rs3730051	1.00[ASW][hapmap];0.82[CEU][hapmap];0.80[CHB][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.86[MEX][hapmap];0.90[TSI][hapmap];0.95[YRI][hapmap];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4239504	0.82[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.80[ASN][1000 genomes]
rs4239506	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4257318	0.90[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4277441	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4332845	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4337402	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4490099	0.90[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4499338	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4558508	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];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802070	0.82[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap]
rs4802071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802073	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4802074	1.00[ASW][hapmap];0.82[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap];0.81[YRI][hapmap]
rs4803320	1.00[ASW][hapmap];0.82[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6508936	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7248338	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7249146	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.82[ASN][1000 genomes]
rs7250897	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];0.94[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7255581	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7257972	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7260106	0.84[ASN][1000 genomes]
rs7260517	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs748236	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7508604	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs8100018	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs8102171	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8104727	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8110888	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.84[ASN][1000 genomes]
rs969531	1.00[ASW][hapmap];0.95[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9749283	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1826663	chr19:40529943-41023601	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv2758499	chr19:40612420-40839520	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	esv2758761	chr19:40612420-40839520	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv911699	chr19:40691632-40816530	Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	esv1833489	chr19:40722123-40923908	Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv1064502	chr19:40758049-40781360	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1063993	chr19:40763787-40781360	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv1059884	chr19:40763839-40781360	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3730050	C19orf47	cis	multi-tissue	Pritchard
rs3730050	ZNF221	cis	parietal	SCAN
rs3730050	SYMPK	cis	cerebellum	SCAN
rs3730050	IGFL4	cis	parietal	SCAN
rs3730050	C19orf47	cis	lymphoblastoid	seeQTL
rs3730050	TMEM91	cis	parietal	SCAN
rs3730050	ERCC1	cis	parietal	SCAN
rs3730050	FLJ36888	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40751200-40771200	Weak transcription	Fetal Heart	heart
2	chr19:40753000-40772000	Weak transcription	Fetal Brain Male	brain
3	chr19:40759800-40775400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr19:40759800-40780600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr19:40762000-40779800	Weak transcription	Stomach Mucosa	stomach
6	chr19:40762200-40772200	Weak transcription	NH-A	brain
7	chr19:40762800-40777600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr19:40762800-40780800	Weak transcription	Small Intestine	intestine
9	chr19:40763200-40774000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr19:40763400-40771000	Weak transcription	Primary hematopoietic stem cells	blood
11	chr19:40763600-40777800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr19:40763800-40777600	Weak transcription	Hela-S3	cervix
13	chr19:40763800-40777600	Weak transcription	HMEC	breast
14	chr19:40765400-40777800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr19:40766200-40788600	Weak transcription	HSMMtube	muscle
16	chr19:40766800-40771400	Strong transcription	Duodenum Smooth Muscle	Duodenum
17	chr19:40766800-40776600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr19:40767000-40776200	Strong transcription	Primary T cells from cord blood	blood
19	chr19:40767400-40771000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr19:40767400-40771200	Strong transcription	Placenta Amnion	Placenta Amnion
21	chr19:40767400-40774800	Strong transcription	Thymus	Thymus
22	chr19:40767600-40771600	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr19:40767600-40772200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr19:40767600-40774800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr19:40767600-40779600	Strong transcription	Fetal Stomach	stomach
26	chr19:40767800-40771000	Strong transcription	Primary B cells from cord blood	blood
27	chr19:40767800-40771400	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr19:40767800-40771400	Strong transcription	Stomach Smooth Muscle	stomach
29	chr19:40767800-40780400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr19:40768000-40771000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr19:40768000-40771200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr19:40768000-40771200	Strong transcription	Fetal Thymus	thymus
33	chr19:40768000-40771600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr19:40768000-40771600	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr19:40768000-40771600	Strong transcription	A549	lung
36	chr19:40768000-40771800	Strong transcription	K562	blood
37	chr19:40768000-40772400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr19:40768000-40772400	Strong transcription	Placenta	Placenta
39	chr19:40768000-40774400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr19:40768200-40771000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr19:40768200-40771000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr19:40768200-40771200	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr19:40768200-40771200	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr19:40768200-40771200	Strong transcription	Muscle Satellite Cultured Cells	--
45	chr19:40768200-40771200	Strong transcription	Liver	Liver
46	chr19:40768200-40771200	Strong transcription	Pancreas	Pancrea
47	chr19:40768200-40771200	Strong transcription	Rectal Smooth Muscle	rectum
48	chr19:40768200-40771200	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr19:40768200-40771400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr19:40768200-40771400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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