Variant report

Variant	rs13219307
Chromosome Location	chr6:35000663-35000664
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:26947473..26948028-chr6:34999920..35000846,2	MCF-7	breast:
2	chr6:34998385..35000765-chr6:35002872..35004521,2	MCF-7	breast:
3	chr6:34994556..34998578-chr6:34998827..35004744,6	K562	blood:

Extended variants
information (count: 95 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1051115	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11552398	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11961798	1.00[JPT][hapmap]
rs11964930	1.00[JPT][hapmap]
rs13196367	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13196771	0.81[ASN][1000 genomes]
rs13196785	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13199238	1.00[JPT][hapmap]
rs13203612	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs13205210	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13206654	0.83[ASN][1000 genomes]
rs13207848	0.92[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[ASN][1000 genomes]
rs13211490	1.00[JPT][hapmap]
rs13214114	0.83[ASN][1000 genomes]
rs13216424	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs13217848	1.00[JPT][hapmap]
rs16871749	1.00[JPT][hapmap];0.81[TSI][hapmap];0.83[ASN][1000 genomes]
rs16871809	1.00[JPT][hapmap];0.81[TSI][hapmap];0.83[ASN][1000 genomes]
rs16871814	1.00[JPT][hapmap];0.81[TSI][hapmap];0.83[ASN][1000 genomes]
rs16896559	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1747516	0.83[ASN][1000 genomes]
rs1747517	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs17610836	0.83[ASN][1000 genomes]
rs17611877	0.83[ASN][1000 genomes]
rs1880090	0.85[CHB][hapmap]
rs2177380	0.92[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs2234044	1.00[JPT][hapmap];0.81[TSI][hapmap];0.83[ASN][1000 genomes]
rs2234045	1.00[JPT][hapmap]
rs2296361	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2296362	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2395608	0.81[ASN][1000 genomes]
rs2395610	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2494098	0.80[ASN][1000 genomes]
rs2762336	0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2820225	0.83[ASN][1000 genomes]
rs34069418	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34103100	0.81[ASN][1000 genomes]
rs34208177	0.83[ASN][1000 genomes]
rs34250961	0.83[ASN][1000 genomes]
rs34715060	0.81[ASN][1000 genomes]
rs34930033	0.83[ASN][1000 genomes]
rs35095464	0.83[ASN][1000 genomes]
rs35693439	0.81[ASN][1000 genomes]
rs3734261	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3734266	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3756856	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs41270050	0.83[ASN][1000 genomes]
rs4628094	0.83[ASN][1000 genomes]
rs4646933	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs57111149	0.83[ASN][1000 genomes]
rs6457796	0.85[CHB][hapmap]
rs6457797	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs66579470	0.81[ASN][1000 genomes]
rs67167177	0.83[ASN][1000 genomes]
rs67638810	0.83[ASN][1000 genomes]
rs67941146	0.81[ASN][1000 genomes]
rs6899618	0.83[ASN][1000 genomes]
rs6906666	1.00[JPT][hapmap];0.81[TSI][hapmap];0.83[ASN][1000 genomes]
rs6913286	0.83[ASN][1000 genomes]
rs6913975	0.83[ASN][1000 genomes]
rs6915649	1.00[JPT][hapmap]
rs6925175	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6926532	0.83[ASN][1000 genomes]
rs6936337	0.83[ASN][1000 genomes]
rs6942104	0.83[ASN][1000 genomes]
rs728238	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs72896254	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72897804	0.83[ASN][1000 genomes]
rs72901705	0.82[ASN][1000 genomes]
rs7739385	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7743949	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7761391	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7766770	0.81[ASN][1000 genomes]
rs7767073	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs820061	0.88[ASN][1000 genomes]
rs820062	0.92[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs820063	0.88[ASN][1000 genomes]
rs820065	0.83[CHB][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs820066	0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs820067	0.88[ASN][1000 genomes]
rs820069	0.92[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.88[ASN][1000 genomes]
rs820072	0.88[ASN][1000 genomes]
rs820083	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs820095	0.92[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.80[MKK][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs820099	1.00[JPT][hapmap];0.81[TSI][hapmap];0.83[ASN][1000 genomes]
rs820100	0.83[ASN][1000 genomes]
rs820101	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs820103	0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs843937	0.88[ASN][1000 genomes]
rs865352	0.94[EUR][1000 genomes]
rs9462053	0.81[ASN][1000 genomes]
rs9462054	0.81[ASN][1000 genomes]
rs9469950	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022844	chr6:34317219-35060519	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv538195	chr6:34317219-35060519	Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13219307	TCP11	cis	lymphoblastoid	seeQTL
rs13219307	TCP11	cis	multi-tissue	Pritchard

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:34939400-35016000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr6:34963600-35006600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr6:34979800-35002000	Weak transcription	GM12878-XiMat	blood
4	chr6:34986200-35015000	Weak transcription	Primary B cells from peripheral blood	blood
5	chr6:34986400-35011800	Weak transcription	Dnd41	blood
6	chr6:34986800-35014800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr6:34987000-35009000	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr6:34987000-35015800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr6:34987400-35015800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr6:34989000-35002800	Weak transcription	Fetal Thymus	thymus
11	chr6:34989400-35002200	Weak transcription	Thymus	Thymus
12	chr6:34990800-35002800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr6:34992800-35011800	Weak transcription	Brain Germinal Matrix	brain
14	chr6:34993400-35002600	Weak transcription	Small Intestine	intestine
15	chr6:34993800-35000800	Weak transcription	Fetal Brain Female	brain
16	chr6:34993800-35006000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr6:34993800-35014600	Weak transcription	Fetal Brain Male	brain
18	chr6:34994000-35002400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr6:34994200-35004000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr6:34994200-35014400	Weak transcription	NHLF	lung
21	chr6:34994400-35001000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr6:34994400-35003200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr6:34994400-35005400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr6:34994600-35036000	Weak transcription	K562	blood
25	chr6:34995000-35002200	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr6:34995000-35002200	Weak transcription	NHDF-Ad	bronchial
27	chr6:34995000-35002400	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr6:34995000-35005600	Weak transcription	Osteobl	bone
29	chr6:34995000-35005800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr6:34995000-35013800	Weak transcription	Hela-S3	cervix
31	chr6:34995200-35002200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr6:34995200-35003400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:34995400-35002400	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr6:34995600-35002200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr6:34995600-35002600	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr6:34995600-35002800	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr6:34995600-35003800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr6:34995800-35001000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr6:34995800-35002200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr6:34996000-35002800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr6:34996000-35015200	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr6:34996200-35001200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr6:34996200-35001600	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr6:34996200-35001600	Weak transcription	Gastric	stomach
45	chr6:34996200-35001600	Weak transcription	Stomach Mucosa	stomach
46	chr6:34996200-35002200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr6:34996200-35002600	Weak transcription	Pancreas	Pancrea
48	chr6:34996200-35002600	Weak transcription	Psoas Muscle	Psoas
49	chr6:34996200-35005400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr6:34996200-35010000	Weak transcription	Ovary	ovary

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links