Variant report

Variant	rs7105804
Chromosome Location	chr11:93472964-93472965
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	chr11:93469329-93475448	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr11:93470883-93475415	HCT-116	colon:	n/a	n/a
3	MXI1	chr11:93472666-93475366	GM12878	blood:	n/a	chr11:93474081-93474090 chr11:93474081-93474090 chr11:93474083-93474092
4	POLR2A	chr11:93472270-93473102	GM12892	blood:	n/a	n/a
5	POLR2A	chr11:93471623-93475375	GM19099	blood:	n/a	n/a
6	CHD1	chr11:93472376-93475351	GM12878	blood:	n/a	chr11:93474702-93474711 chr11:93474437-93474447
7	POLR2A	chr11:93458130-93475423	Hela-S3	cervix:	n/a	n/a
8	POLR2A	chr11:93465161-93475401	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr11:93471612-93475305	SK-N-MC	brain:	n/a	n/a
10	POLR2A	chr11:93465505-93475492	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr11:93472841-93475410	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr11:93460849-93475367	GM18505	blood:	n/a	n/a
13	CTCF	chr11:93472820-93472970	RPTEC	kidney:	n/a	n/a
14	POLR2A	chr11:93460250-93475527	HepG2	liver:	n/a	n/a
15	POLR2A	chr11:93472678-93473088	MCF-7	breast:	n/a	n/a
16	POLR2A	chr11:93472775-93473001	SK-N-SH	brain:	n/a	n/a
17	POLR2A	chr11:93469624-93475431	PANC-1	pancreas:	n/a	n/a
18	POLR2A	chr11:93471000-93475242	HUVEC	blood vessel:	n/a	n/a
19	POLR2A	chr11:93459876-93475383	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr11:93469231-93475445	PFSK-1	brain:	n/a	n/a
21	POLR2A	chr11:93466346-93475414	GM12891	blood:	n/a	n/a
22	TCF7L2	chr11:93472693-93473641	Hela-S3	cervix:	n/a	chr11:93472856-93472866 chr11:93472857-93472866 chr11:93472855-93472869 chr11:93472854-93472870 chr11:93472858-93472867 chr11:93472854-93472870
23	POLR2A	chr11:93472809-93475257	GM15510	blood:	n/a	n/a
24	POLR2A	chr11:93460023-93475421	GM12878	blood:	n/a	n/a
25	POLR2A	chr11:93472859-93475315	K562	blood:	n/a	n/a
26	POLR2A	chr11:93472749-93476093	HepG2	liver:	n/a	n/a
27	POLR2A	chr11:93472300-93475117	HUVEC	blood vessel:	n/a	n/a
28	ATF2	chr11:93472474-93475177	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr11:93470422-93475330	K562	blood:	n/a	n/a
30	POLR2A	chr11:93472326-93475450	GM12892	blood:	n/a	n/a
31	TAF7	chr11:93471730-93475014	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr11:93472800-93473725	HepG2	liver:	n/a	n/a
33	POLR2A	chr11:93460630-93475546	PFSK-1	brain:	n/a	n/a
34	TCF7L2	chr11:93472736-93472999	PANC-1	pancreas:	n/a	chr11:93472856-93472866 chr11:93472857-93472866 chr11:93472855-93472869 chr11:93472854-93472870 chr11:93472858-93472867 chr11:93472854-93472870
35	HEY1	chr11:93472308-93475444	HepG2	liver:	n/a	n/a
36	POLR2A	chr11:93470252-93475435	HUVEC	blood vessel:	n/a	n/a
37	POLR2A	chr11:93459823-93475456	HepG2	liver:	n/a	n/a
38	POLR2A	chr11:93471815-93475055	A549	lung:	n/a	n/a
39	BRCA1	chr11:93472565-93475496	Hela-S3	cervix:	n/a	chr11:93474702-93474711
40	POLR2A	chr11:93469412-93475274	GM12892	blood:	n/a	n/a
41	POLR2A	chr11:93459661-93475348	K562	blood:	n/a	n/a
42	POLR2A	chr11:93472842-93475350	GM18951	blood:	n/a	n/a
43	POLR2A	chr11:93470174-93475516	PANC-1	pancreas:	n/a	n/a
44	CHD1	chr11:93469865-93475272	H1-hESC	embryonic stem cell:	n/a	chr11:93474702-93474711 chr11:93474437-93474447
45	MYBL2	chr11:93472874-93473588	HepG2	liver:	n/a	n/a
46	POLR2A	chr11:93471468-93475392	GM12892	blood:	n/a	n/a
47	POLR2A	chr11:93472876-93475095	H1-hESC	embryonic stem cell:	n/a	n/a
48	ATF2	chr11:93472924-93473531	GM12878	blood:	n/a	n/a
49	POLR2A	chr11:93472648-93473125	HUVEC	blood vessel:	n/a	n/a
50	POLR2A	chr11:93472718-93475483	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:93472800..93476056-chr11:93515203..93522725,16	MCF-7	breast:
2	chr11:93472896..93475000-chr11:93521473..93523956,3	K562	blood:
3	chr11:93472782..93475284-chr12:120730109..120732929,2	MCF-7	breast:
4	chr11:93274349..93277500-chr11:93472599..93475364,3	K562	blood:
5	chr11:93472961..93474532-chr11:93613286..93616036,2	K562	blood:
6	chr11:93471347..93475237-chr11:93486063..93491649,6	K562	blood:
7	chr11:93472589..93476859-chr11:93528988..93534877,8	K562	blood:
8	chr11:93462890..93477443-chr11:93512595..93526939,73	K562	blood:
9	chr11:93472413..93474850-chr11:93477709..93480682,4	MCF-7	breast:
10	chr11:93472354..93474057-chr11:93524242..93526809,2	K562	blood:
11	chr11:93468490..93476714-chr11:93515963..93520210,25	MCF-7	breast:
12	chr11:93393010..93396864-chr11:93472820..93475395,3	K562	blood:
13	chr11:93472702..93474263-chr8:129062907..129064427,2	K562	blood:
14	chr11:93452361..93455098-chr11:93472021..93474456,2	MCF-7	breast:
15	chr11:93472363..93476142-chr11:93531511..93536193,5	K562	blood:
16	chr11:93472790..93475144-chr7:30540146..30542802,2	MCF-7	breast:
17	chr11:93429389..93432729-chr11:93472370..93474745,3	K562	blood:
18	chr11:93468648..93476533-chr11:93513626..93520226,41	K562	blood:
19	chr11:93372093..93374223-chr11:93472267..93473882,2	K562	blood:

Variant related genes	Relation type
TAF1D	TF binding region
C11orf54	TF binding region
SNORA40	TF binding region
ENSG00000182919	Chromatin interaction
ENSG00000265292	Chromatin interaction
ENSG00000199875	Chromatin interaction
ENSG00000166004	Chromatin interaction
ENSG00000166002	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000254911	Chromatin interaction
ENSG00000006625	Chromatin interaction
ENSG00000042429	Chromatin interaction
ENSG00000238437	Chromatin interaction
ENSG00000166012	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10160552	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10765620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10831089	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10831091	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10831093	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11020484	0.89[ASW][hapmap];0.85[CEU][hapmap]
rs1939565	0.90[EUR][1000 genomes]
rs1944104	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4146891	0.85[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs61229806	0.91[EUR][1000 genomes]
rs6483261	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6483262	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7119996	0.85[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.94[EUR][1000 genomes]
rs7939460	0.89[CEU][hapmap];0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7950893	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898181	chr11:93072843-93662459	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv898182	chr11:93381845-93637462	Strong transcription Genic enhancers Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
3	nsv832232	chr11:93401314-93549438	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs7105804	C11orf54	cis	Heart Left Ventricle	GTEx
rs7105804	C11orf54	cis	parietal	SCAN
rs7105804	C11orf54	cis	lung	GTEx
rs7105804	C11orf54	cis	lymphoblastoid	seeQTL
rs7105804	C11orf54	cis	cerebellum	SCAN
rs7105804	SCARNA9	cis	parietal	SCAN
rs7105804	PIWIL4	cis	parietal	SCAN
rs7105804	ANKRD49	cis	parietal	SCAN
rs7105804	SCARNA9	cis	cerebellum	SCAN
rs7105804	MED17	cis	cerebellum	SCAN
rs7105804	MED17	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:93450600-93473000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:93459400-93473000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:93466600-93473400	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr11:93468000-93473200	Transcr. at gene 5' and 3'	HUVEC	blood vessel
5	chr11:93468000-93473600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr11:93468800-93473600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
7	chr11:93469000-93473200	Weak transcription	Lung	lung
8	chr11:93469200-93473000	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr11:93469200-93473600	Transcr. at gene 5' and 3'	A549	lung
10	chr11:93469200-93473600	Transcr. at gene 5' and 3'	Osteobl	bone
11	chr11:93469200-93474000	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
12	chr11:93469400-93473600	Transcr. at gene 5' and 3'	K562	blood
13	chr11:93469400-93474000	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
14	chr11:93469400-93474400	Transcr. at gene 5' and 3'	Dnd41	blood
15	chr11:93469800-93473000	Transcr. at gene 5' and 3'	HMEC	breast
16	chr11:93469800-93473200	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr11:93469800-93473400	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr11:93469800-93473400	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr11:93470000-93473000	Genic enhancers	Primary B cells from peripheral blood	blood
20	chr11:93470000-93473200	Transcr. at gene 5' and 3'	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr11:93470200-93473000	Transcr. at gene 5' and 3'	Hela-S3	cervix
22	chr11:93470400-93473400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
23	chr11:93470400-93473400	Transcr. at gene 5' and 3'	NHEK	skin
24	chr11:93470400-93473600	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
25	chr11:93470400-93473600	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
26	chr11:93470400-93473800	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
27	chr11:93470800-93473000	Enhancers	Fetal Heart	heart
28	chr11:93470800-93473800	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
29	chr11:93470800-93475800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr11:93471000-93473600	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
31	chr11:93471000-93474600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
32	chr11:93471200-93473200	Active TSS	Right Ventricle	heart
33	chr11:93471200-93474000	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr11:93471400-93473000	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
35	chr11:93471400-93473000	Genic enhancers	Primary monocytes fromperipheralblood	blood
36	chr11:93471400-93473200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr11:93471600-93473600	Transcr. at gene 5' and 3'	Primary T killer memory cells from peripheral blood	blood
38	chr11:93471600-93474000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr11:93471600-93474200	Transcr. at gene 5' and 3'	ES-I3 Cell Line	embryonic stem cell
40	chr11:93471800-93473000	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr11:93471800-93473200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
42	chr11:93471800-93473200	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
43	chr11:93471800-93473600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr11:93471800-93473600	Transcr. at gene 5' and 3'	HSMM	muscle
45	chr11:93471800-93473600	Transcr. at gene 5' and 3'	NHLF	lung
46	chr11:93471800-93473800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
47	chr11:93472000-93473200	Enhancers	Aorta	Aorta
48	chr11:93472000-93473200	Enhancers	Placenta Amnion	Placenta Amnion
49	chr11:93472000-93475800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr11:93472200-93473000	Weak transcription	Sigmoid Colon	Sigmoid Colon

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