Variant report

Variant	rs4873770
Chromosome Location	chr8:48846258-48846259
allele	C/T
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:5)
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	POLR2A	chr8:48846229-48846264	MCF-7	breast:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr8:48839901..48842172-chr8:48844421..48847174,2	K562	blood:
2	chr8:48846197..48849935-chr8:48851023..48856886,6	K562	blood:
3	chr8:48840672..48844205-chr8:48845279..48848324,4	K562	blood:
4	chr8:48845787..48848384-chr8:48854733..48856494,2	MCF-7	breast:
5	chr8:48843317..48847035-chr8:48871031..48874795,6	K562	blood:

No data

Variant related genes	Relation type
PRKDC	TF binding region
ENSG00000104738	Chromatin interaction
ENSG00000253729	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10088698	0.80[GIH][hapmap];0.83[TSI][hapmap]
rs10091017	0.85[EUR][1000 genomes]
rs10097783	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10106778	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10481294	0.90[EUR][1000 genomes]
rs10808897	1.00[CEU][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap]
rs10958438	0.80[EUR][1000 genomes]
rs11986191	0.80[EUR][1000 genomes]
rs12156246	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12334811	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13251871	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1551655	1.00[CEU][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs17334535	0.86[EUR][1000 genomes]
rs1894311	1.00[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28457765	0.82[CEU][hapmap];0.95[MEX][hapmap]
rs28578331	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28641816	1.00[CEU][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.80[EUR][1000 genomes]
rs3614	1.00[CEU][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs3829985	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4618724	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4873266	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4873771	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4873773	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6993292	0.80[EUR][1000 genomes]
rs72647908	0.92[EUR][1000 genomes]
rs72647909	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72647913	0.89[EUR][1000 genomes]
rs72647914	0.95[EUR][1000 genomes]
rs72647916	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72647918	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72647922	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7824066	0.84[EUR][1000 genomes]
rs7838910	1.00[CEU][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs8178016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8178079	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8178095	1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8178097	0.87[EUR][1000 genomes]
rs8178158	0.88[AMR][1000 genomes]
rs8178238	1.00[CEU][hapmap]
rs9657054	1.00[CEU][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs9918758	1.00[CEU][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]

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	esv1803608	chr8:48506628-48874811	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1021389	chr8:48700970-48880931	Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv539599	chr8:48700970-48880931	Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv931032	chr8:48744329-49091359	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	esv2758156	chr8:48788293-49008014	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	esv2759611	chr8:48788293-49008014	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv427820	chr8:48788293-49008014	Strong transcription Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
8	nsv831309	chr8:48815290-48977856	Strong transcription Genic enhancers Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4873770	TPM2	trans	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:48726400-48870400	Strong transcription	Primary T helper cells fromperipheralblood	blood
2	chr8:48730000-48871600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr8:48739600-48870600	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr8:48739800-48870400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr8:48785200-48859000	Strong transcription	Fetal Muscle Trunk	muscle
6	chr8:48793800-48870400	Strong transcription	HUES64 Cell Line	embryonic stem cell
7	chr8:48793800-48870800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
8	chr8:48800600-48854000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr8:48814000-48853800	Strong transcription	A549	lung
10	chr8:48815400-48851600	Weak transcription	Stomach Mucosa	stomach
11	chr8:48820000-48857400	Strong transcription	Primary T helper cells PMA-I stimulated	--
12	chr8:48820000-48871000	Strong transcription	Fetal Intestine Large	intestine
13	chr8:48820200-48853400	Strong transcription	Fetal Thymus	thymus
14	chr8:48820400-48854800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr8:48820400-48870000	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr8:48820400-48870000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr8:48822400-48870800	Strong transcription	Liver	Liver
18	chr8:48822600-48860000	Strong transcription	Hela-S3	cervix
19	chr8:48822600-48870600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr8:48822600-48870800	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr8:48823200-48854600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr8:48823200-48870600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr8:48824200-48870200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr8:48824800-48870000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr8:48826600-48848200	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr8:48830600-48857400	Strong transcription	HSMM	muscle
27	chr8:48830800-48857200	Strong transcription	Duodenum Mucosa	Duodenum
28	chr8:48831400-48859000	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr8:48833800-48849400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr8:48833800-48870800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr8:48833800-48870800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr8:48834000-48853400	Strong transcription	Placenta	Placenta
33	chr8:48834000-48856800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr8:48834000-48869200	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr8:48834000-48869400	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr8:48834000-48869400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr8:48834400-48870200	Strong transcription	Primary B cells from peripheral blood	blood
38	chr8:48834600-48853200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr8:48834800-48849200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr8:48835200-48849200	Strong transcription	Fetal Lung	lung
41	chr8:48835400-48870200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr8:48835800-48871600	Strong transcription	Primary B cells from cord blood	blood
43	chr8:48836000-48856800	Strong transcription	Osteobl	bone
44	chr8:48836400-48853800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr8:48836400-48854600	Weak transcription	Small Intestine	intestine
46	chr8:48836600-48853800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr8:48836800-48853800	Strong transcription	HMEC	breast
48	chr8:48837400-48860400	Strong transcription	Primary hematopoietic stem cells	blood
49	chr8:48838800-48854000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr8:48838800-48854000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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