Variant report

Variant	rs4802071
Chromosome Location	chr19:40764215-40764216
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:40731149-40781638	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:40763137..40764665-chr19:40768633..40770903,2	MCF-7	breast:
2	chr19:40754146..40755800-chr19:40763608..40765954,2	K562	blood:
3	chr19:40763181..40767170-chr19:40767340..40771711,5	K562	blood:

Variant related genes	Relation type
AKT2	TF binding region
ENSG00000105221	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10402740	0.81[JPT][hapmap]
rs10405207	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1129156	0.82[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap]
rs11668242	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11880261	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12974529	0.91[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12981110	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2304184	0.82[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs2304189	0.89[CHB][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs339526	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs3730050	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]
rs3730051	0.82[CEU][hapmap];0.80[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4239504	0.82[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs4239506	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4257318	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4277441	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4332845	0.96[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];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4490099	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4499338	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4558508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[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]
rs4802073	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4802074	0.82[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap]
rs4803320	0.82[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.91[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];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7248338	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7249146	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7250897	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[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];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7260106	0.84[ASN][1000 genomes]
rs7260517	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs748236	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7508604	0.88[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[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8104727	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8110888	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs969531	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9749283	0.97[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4802071	FLJ36888	cis	multi-tissue	Pritchard
rs4802071	C19orf47	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	chr19:40753200-40764600	Strong transcription	Primary T cells from cord blood	blood
4	chr19:40753800-40764400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr19:40755600-40764600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr19:40759800-40770600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr19:40759800-40775400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr19:40759800-40780600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr19:40760600-40764400	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr19:40761800-40768200	Weak transcription	HSMM	muscle
11	chr19:40762000-40779800	Weak transcription	Stomach Mucosa	stomach
12	chr19:40762200-40765600	Weak transcription	HSMMtube	muscle
13	chr19:40762200-40772200	Weak transcription	NH-A	brain
14	chr19:40762400-40768600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr19:40762600-40765000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr19:40762600-40767400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr19:40762600-40768000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr19:40762600-40768200	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr19:40762600-40768200	Weak transcription	Aorta	Aorta
20	chr19:40762600-40768200	Weak transcription	HUVEC	blood vessel
21	chr19:40762800-40766800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr19:40762800-40767400	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr19:40762800-40768000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr19:40762800-40768200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr19:40762800-40768200	Weak transcription	Rectal Smooth Muscle	rectum
26	chr19:40762800-40768200	Weak transcription	HepG2	liver
27	chr19:40762800-40768400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr19:40762800-40768400	Weak transcription	Fetal Kidney	kidney
29	chr19:40762800-40777600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr19:40762800-40780800	Weak transcription	Small Intestine	intestine
31	chr19:40763000-40764400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr19:40763000-40767400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr19:40763000-40767600	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr19:40763000-40767600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr19:40763000-40768000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr19:40763000-40768200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr19:40763000-40768200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr19:40763000-40768200	Weak transcription	Ovary	ovary
39	chr19:40763000-40768200	Weak transcription	NHDF-Ad	bronchial
40	chr19:40763000-40768400	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr19:40763000-40768400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr19:40763000-40768400	Weak transcription	Brain Angular Gyrus	brain
43	chr19:40763000-40768400	Weak transcription	Brain Germinal Matrix	brain
44	chr19:40763000-40768400	Weak transcription	Brain Substantia Nigra	brain
45	chr19:40763000-40768400	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr19:40763000-40768600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr19:40763000-40768800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr19:40763000-40768800	Weak transcription	Fetal Lung	lung
49	chr19:40763000-40769600	Weak transcription	Colon Smooth Muscle	Colon
50	chr19:40763200-40766600	Weak transcription	Stomach Smooth Muscle	stomach

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