Variant report

Variant	rs6993483
Chromosome Location	chr8:48776189-48776190
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:48709573..48711482-chr8:48774056..48776581,2	K562	blood:
2	chr8:48775024..48776712-chr8:48799790..48801696,2	MCF-7	breast:

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10088698	0.84[JPT][hapmap];0.83[TSI][hapmap]
rs10091017	0.94[ASW][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap];0.91[LWK][hapmap];0.93[MKK][hapmap];0.96[YRI][hapmap];0.88[AMR][1000 genomes]
rs10092880	1.00[CEU][hapmap]
rs10097508	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10097783	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10106778	1.00[CEU][hapmap];0.92[CHB][hapmap];0.82[CHD][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10109158	0.92[ASN][1000 genomes]
rs10481294	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10808897	0.94[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.82[CHD][hapmap];0.92[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap]
rs10958274	1.00[CEU][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs10958438	0.86[AMR][1000 genomes]
rs11986191	0.84[AMR][1000 genomes]
rs12156246	0.85[EUR][1000 genomes]
rs12334811	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13251871	0.85[EUR][1000 genomes]
rs1487438	1.00[CEU][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs1551655	0.94[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs1894311	1.00[CEU][hapmap];0.92[CHB][hapmap];0.82[CHD][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs1903082	0.83[AMR][1000 genomes]
rs28485144	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28641816	0.94[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs28702696	0.86[AMR][1000 genomes]
rs28795698	0.83[ASN][1000 genomes]
rs28809491	0.83[ASN][1000 genomes]
rs3614	0.82[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[JPT][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4521758	0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs4618724	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4873266	1.00[CEU][hapmap];0.92[CHB][hapmap];0.82[CHD][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs4873728	0.87[EUR][1000 genomes]
rs4873737	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4873770	1.00[CEU][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap]
rs4873771	0.85[EUR][1000 genomes]
rs6993292	0.86[AMR][1000 genomes]
rs6995756	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7014544	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7016660	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7017622	0.85[ASN][1000 genomes]
rs72646401	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72647906	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72647908	0.85[EUR][1000 genomes]
rs72647909	0.85[EUR][1000 genomes]
rs72647913	0.82[EUR][1000 genomes]
rs7813617	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7818445	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7824066	0.83[AMR][1000 genomes]
rs7828380	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7830350	0.87[ASN][1000 genomes]
rs7830633	0.87[ASN][1000 genomes]
rs7830743	0.80[EUR][1000 genomes]
rs7831196	0.85[ASN][1000 genomes]
rs7832898	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7838910	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7839407	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7841661	1.00[CEU][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap]
rs8178016	1.00[CEU][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs8178079	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8178095	1.00[CEU][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs8178097	0.80[EUR][1000 genomes]
rs8178158	0.85[EUR][1000 genomes]
rs8178169	0.82[EUR][1000 genomes]
rs8178238	1.00[CEU][hapmap]
rs8178255	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8178258	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9657054	0.94[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes]
rs9918758	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6993483	TPM2	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:48684400-48778800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr8:48684400-48861600	Strong transcription	Dnd41	blood
3	chr8:48685000-48818800	Strong transcription	Fetal Thymus	thymus
4	chr8:48722200-48778600	Strong transcription	Primary monocytes fromperipheralblood	blood
5	chr8:48722600-48798800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr8:48723000-48793400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr8:48726000-48778800	Strong transcription	Primary B cells from peripheral blood	blood
8	chr8:48726200-48793400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr8:48726400-48783200	Strong transcription	GM12878-XiMat	blood
10	chr8:48726400-48870400	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr8:48727400-48777600	Strong transcription	Primary T cells from cord blood	blood
12	chr8:48730000-48871600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr8:48738400-48818800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr8:48738800-48777800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr8:48739600-48778400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr8:48739600-48783200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr8:48739600-48793400	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr8:48739600-48799400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr8:48739600-48822200	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr8:48739600-48870600	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr8:48739800-48779200	Strong transcription	Adipose Nuclei	Adipose
22	chr8:48739800-48793400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr8:48739800-48870400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr8:48745400-48777400	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr8:48745800-48777800	Strong transcription	HSMM	muscle
26	chr8:48751000-48777600	Strong transcription	A549	lung
27	chr8:48751400-48805800	Strong transcription	Fetal Lung	lung
28	chr8:48754000-48782400	Strong transcription	Liver	Liver
29	chr8:48755600-48781800	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr8:48756600-48793400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr8:48757600-48777400	Strong transcription	Duodenum Mucosa	Duodenum
32	chr8:48758200-48777800	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr8:48758200-48799600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr8:48759000-48779000	Strong transcription	Placenta	Placenta
35	chr8:48759200-48777200	Strong transcription	K562	blood
36	chr8:48759200-48777400	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr8:48759200-48785000	Strong transcription	Hela-S3	cervix
38	chr8:48759600-48777600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr8:48759600-48783800	Strong transcription	Fetal Muscle Trunk	muscle
40	chr8:48759600-48784200	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr8:48759800-48777600	Strong transcription	Fetal Brain Female	brain
42	chr8:48759800-48778800	Strong transcription	Fetal Intestine Large	intestine
43	chr8:48759800-48783600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr8:48759800-48784000	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr8:48759800-48808400	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr8:48760000-48777200	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr8:48760000-48777600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr8:48760200-48783600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr8:48760400-48777400	Strong transcription	Ovary	ovary
50	chr8:48760400-48777800	Strong transcription	Duodenum Smooth Muscle	Duodenum

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