Variant report

Variant	rs1671063
Chromosome Location	chr11:66272142-66272143
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	chr11:66271226..66274092-chr11:66277706..66279394,2	K562	blood:
2	chr11:66245898..66247692-chr11:66270786..66272292,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254986	Chromatin interaction
ENSG00000174483	Chromatin interaction
ENSG00000255517	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10736656	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10791881	0.86[ASW][hapmap]
rs10791882	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12577111	0.81[JPT][hapmap];0.86[MKK][hapmap]
rs1671062	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1671064	0.86[CHB][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.82[ASN][1000 genomes]
rs1671065	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1700184	0.80[EUR][1000 genomes]
rs1700189	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1791684	0.81[JPT][hapmap]
rs1791686	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1791687	0.84[EUR][1000 genomes]
rs1815739	0.86[CHB][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.82[ASN][1000 genomes]
rs2000939	0.83[ASN][1000 genomes]
rs2276138	0.81[JPT][hapmap]
rs2279863	0.95[JPT][hapmap];0.83[MEX][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2444846	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3018318	0.81[ASN][1000 genomes]
rs3107024	0.84[ASN][1000 genomes]
rs3741363	0.81[JPT][hapmap]
rs486584	0.86[CHB][hapmap];0.85[JPT][hapmap];0.84[MKK][hapmap]
rs4930387	0.81[JPT][hapmap];0.80[YRI][hapmap]
rs509556	0.86[CHB][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.84[MKK][hapmap];0.87[YRI][hapmap];0.83[ASN][1000 genomes]
rs540874	0.86[CHB][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.82[ASN][1000 genomes]
rs545009	0.82[ASN][1000 genomes]
rs560556	0.86[CHB][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.82[ASN][1000 genomes]
rs572846	0.86[CHB][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.82[ASN][1000 genomes]
rs577023	0.80[JPT][hapmap]
rs580910	0.86[MKK][hapmap]
rs615205	0.82[ASN][1000 genomes]
rs618838	0.81[CHB][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap]
rs630021	0.81[ASN][1000 genomes]
rs677488	0.86[CHB][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.83[ASN][1000 genomes]
rs678397	0.86[CHB][hapmap];0.80[CHD][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.83[ASN][1000 genomes]
rs7925093	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7925108	0.88[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8432	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3392427	chr11:65981489-66273695	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	118 gene(s)	inside rSNPs	diseases
2	nsv897771	chr11:66011280-66362997	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
3	nsv897780	chr11:66083129-66362997	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
4	nsv832193	chr11:66120339-66278805	Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
5	nsv468601	chr11:66234023-66296114	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv555224	chr11:66234023-66296114	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	nsv522277	chr11:66234023-66493825	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1671063	CCS	Cis_1M	lymphoblastoid	RTeQTL
rs1671063	CTD-3074O7.5	cis	Whole Blood	GTEx
rs1671063	CTD-3074O7.2	cis	Muscle Skeletal	GTEx
rs1671063	ACTN3	cis	Muscle Skeletal	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:66248600-66277600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr11:66248600-66277600	Weak transcription	Fetal Brain Male	brain
3	chr11:66248600-66277600	Weak transcription	Fetal Lung	lung
4	chr11:66248600-66278000	Weak transcription	NHDF-Ad	bronchial
5	chr11:66248800-66277600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr11:66248800-66277600	Weak transcription	K562	blood
7	chr11:66249800-66273200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr11:66251200-66277600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr11:66251800-66274600	Strong transcription	Fetal Stomach	stomach
10	chr11:66254400-66272600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr11:66255800-66277800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr11:66259600-66277600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr11:66261000-66272600	Weak transcription	HSMM	muscle
14	chr11:66261000-66277800	Weak transcription	Psoas Muscle	Psoas
15	chr11:66261200-66272400	Weak transcription	Colon Smooth Muscle	Colon
16	chr11:66261200-66277800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr11:66261200-66278000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr11:66261600-66277600	Weak transcription	Stomach Mucosa	stomach
19	chr11:66261800-66272400	Weak transcription	HepG2	liver
20	chr11:66261800-66277800	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr11:66262400-66277600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr11:66263400-66272200	Weak transcription	A549	lung
23	chr11:66263600-66272200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr11:66263600-66272800	Weak transcription	GM12878-XiMat	blood
25	chr11:66263600-66277800	Weak transcription	NH-A	brain
26	chr11:66264600-66278000	Weak transcription	HMEC	breast
27	chr11:66264800-66277600	Weak transcription	Hela-S3	cervix
28	chr11:66264800-66277800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr11:66264800-66277800	Weak transcription	Osteobl	bone
30	chr11:66265000-66272200	Weak transcription	Aorta	Aorta
31	chr11:66265000-66272400	Weak transcription	Brain Angular Gyrus	brain
32	chr11:66265000-66277800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr11:66265200-66272200	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr11:66265200-66272200	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr11:66265200-66272400	Weak transcription	Brain Substantia Nigra	brain
36	chr11:66265200-66277600	Weak transcription	Small Intestine	intestine
37	chr11:66265200-66277800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr11:66266400-66272400	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr11:66266400-66272400	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr11:66266600-66273000	Strong transcription	Fetal Intestine Small	intestine
41	chr11:66266600-66278000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr11:66267000-66272200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr11:66268800-66276800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr11:66269000-66272200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr11:66269000-66273200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr11:66269600-66272800	Strong transcription	Primary T cells from cord blood	blood
47	chr11:66270400-66273000	Strong transcription	Fetal Muscle Leg	muscle
48	chr11:66270400-66277200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr11:66270600-66273000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr11:66270600-66273200	Strong transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links