Variant report

Variant	rs7101788
Chromosome Location	chr11:3855757-3855758
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	CEBPD	chr11:3855683-3856524	K562	blood:	n/a	n/a
2	POLR2A	chr11:3855408-3855940	GM12892	blood:	n/a	n/a
3	SP1	chr11:3855703-3856369	K562	blood:	n/a	chr11:3856005-3856019 chr11:3855928-3855941 chr11:3856009-3856018 chr11:3856180-3856187
4	POLR2A	chr11:3855310-3857244	GM12892	blood:	n/a	n/a
5	MAX	chr11:3855647-3856162	K562	blood:	n/a	n/a
6	POLR2A	chr11:3855271-3857405	HL-60	blood:	n/a	n/a
7	MAFK	chr11:3855598-3856660	K562	blood:	n/a	n/a
8	CEBPD	chr11:3855638-3856719	K562	blood:	n/a	n/a
9	MYC	chr11:3855509-3856682	K562	blood:	n/a	n/a
10	POLR2A	chr11:3855661-3855878	Hela-S3	cervix:	n/a	n/a
11	CEBPB	chr11:3855676-3856189	K562	blood:	n/a	n/a
12	TBP	chr11:3855585-3856662	K562	blood:	n/a	n/a
13	IRF1	chr11:3855432-3856651	K562	blood:	n/a	chr11:3855790-3855799
14	MAZ	chr11:3855600-3856709	K562	blood:	n/a	n/a
15	REST	chr11:3855536-3856194	HL-60	blood:	n/a	chr11:3855808-3855821
16	MAX	chr11:3855689-3856208	NB4	blood:	n/a	n/a
17	STAT5A	chr11:3855620-3856617	K562	blood:	n/a	chr11:3856251-3856260 chr11:3856003-3856015 chr11:3856010-3856022 chr11:3856252-3856261
18	FAM48A	chr11:3855674-3855874	GM12878	blood:	n/a	n/a
19	TEAD4	chr11:3855442-3856970	K562	blood:	n/a	n/a
20	ARID3A	chr11:3855670-3856589	K562	blood:	n/a	n/a
21	TAF1	chr11:3855645-3856078	K562	blood:	n/a	n/a
22	POLR2A	chr11:3855265-3857252	GM12878	blood:	n/a	n/a
23	GATA2	chr11:3855741-3856375	K562	blood:	n/a	chr11:3855851-3855859 chr11:3856032-3856045
24	POLR2A	chr11:3855456-3855873	GM12878	blood:	n/a	n/a
25	MAFF	chr11:3855697-3856069	K562	blood:	n/a	n/a
26	NR2F2	chr11:3855379-3857159	K562	blood:	n/a	n/a
27	ELF1	chr11:3855717-3856103	K562	blood:	n/a	n/a
28	POLR2A	chr11:3855047-3856209	K562	blood:	n/a	n/a
29	MYC	chr11:3855689-3856733	K562	blood:	n/a	n/a
30	UBTF	chr11:3855535-3856667	K562	blood:	n/a	n/a
31	MYC	chr11:3855743-3856191	NB4	blood:	n/a	n/a
32	ELF1	chr11:3855614-3856887	K562	blood:	n/a	n/a
33	POLR2A	chr11:3854589-3857071	GM12878	blood:	n/a	n/a
34	JUN	chr11:3855666-3856968	K562	blood:	n/a	n/a
35	POLR2A	chr11:3855444-3857172	K562	blood:	n/a	n/a
36	TEAD4	chr11:3855667-3856705	K562	blood:	n/a	n/a
37	PML	chr11:3855619-3856917	K562	blood:	n/a	n/a
38	GATA2	chr11:3855678-3856594	K562	blood:	n/a	chr11:3855851-3855859 chr11:3856032-3856045
39	POLR2A	chr11:3855497-3856741	K562	blood:	n/a	n/a
40	UBTF	chr11:3855676-3855947	K562	blood:	n/a	n/a
41	POLR2A	chr11:3855595-3855884	Hela-S3	cervix:	n/a	n/a
42	CUX1	chr11:3855724-3856558	K562	blood:	n/a	n/a
43	IRF1	chr11:3855712-3856863	K562	blood:	n/a	chr11:3855790-3855799
44	TBL1XR1	chr11:3855526-3857219	K562	blood:	n/a	n/a
45	CHD2	chr11:3855717-3856197	K562	blood:	n/a	n/a
46	ZC3H11A	chr11:3855685-3856010	K562	blood:	n/a	n/a
47	SPI1	chr11:3855694-3856719	HL-60	blood:	n/a	chr11:3855699-3855712
48	ZBTB7A	chr11:3855743-3856081	K562	blood:	n/a	n/a
49	MAX	chr11:3855724-3856629	K562	blood:	n/a	n/a
50	GABPA	chr11:3855691-3856081	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:3830424..3832547-chr11:3854238..3857029,2	K562	blood:
2	chr11:3855085..3856960-chr11:3875832..3877363,2	K562	blood:
3	chr11:3855651..3858581-chr11:3874528..3876405,2	K562	blood:
4	chr11:3853798..3856714-chr11:3858547..3860187,2	MCF-7	breast:
5	chr11:3815959..3820545-chr11:3854514..3864703,12	K562	blood:
6	chr11:3815959..3818805-chr11:3854907..3857637,4	K562	blood:
7	chr11:3855443..3857782-chr11:3869074..3871909,2	K562	blood:

Variant related genes	Relation type
RHOG	TF binding region
ENSG00000167323	Chromatin interaction
ENSG00000229368	Chromatin interaction
ENSG00000177105	Chromatin interaction
ENSG00000263421	Chromatin interaction
ENSG00000148985	Chromatin interaction
ENSG00000110713	Chromatin interaction
ENSG00000228661	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1049388	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11029983	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11030043	0.85[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs11030044	1.00[ASN][1000 genomes]
rs11030055	1.00[ASN][1000 genomes]
rs11030173	1.00[ASN][1000 genomes]
rs11600857	1.00[ASN][1000 genomes]
rs11606318	1.00[ASN][1000 genomes]
rs11606483	1.00[ASN][1000 genomes]
rs17173882	1.00[ASN][1000 genomes]
rs17191448	1.00[ASN][1000 genomes]
rs17276405	1.00[ASN][1000 genomes]
rs17276453	1.00[ASN][1000 genomes]
rs4367942	0.85[GIH][hapmap]
rs4910577	1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs4910846	1.00[ASN][1000 genomes]
rs4910852	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910856	1.00[CEU][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4910857	1.00[ASN][1000 genomes]
rs61896929	1.00[ASN][1000 genomes]
rs61896930	1.00[ASN][1000 genomes]
rs61896931	1.00[ASN][1000 genomes]
rs61896953	1.00[ASN][1000 genomes]
rs61896954	1.00[ASN][1000 genomes]
rs61896956	1.00[ASN][1000 genomes]
rs61896957	1.00[ASN][1000 genomes]
rs61896958	1.00[ASN][1000 genomes]
rs61896959	1.00[ASN][1000 genomes]
rs61899361	1.00[ASN][1000 genomes]
rs61899362	1.00[ASN][1000 genomes]
rs61899363	1.00[ASN][1000 genomes]
rs61899392	1.00[ASN][1000 genomes]
rs61899393	1.00[ASN][1000 genomes]
rs6578414	1.00[ASN][1000 genomes]
rs72844340	1.00[ASN][1000 genomes]
rs72844341	1.00[ASN][1000 genomes]
rs73430467	1.00[ASN][1000 genomes]
rs74050940	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049560	chr11:3678259-3980746	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv540907	chr11:3678259-3980746	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1052744	chr11:3739162-4017601	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1047025	chr11:3750969-4017601	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	esv1803195	chr11:3806490-3924156	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv1046065	chr11:3808818-4049150	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats 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 miRNA target site	29 gene(s)	inside rSNPs	diseases
7	nsv540909	chr11:3808818-4049150	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv1038220	chr11:3818041-3860024	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	nsv1044882	chr11:3828986-3860024	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
10	nsv1044360	chr11:3832288-3860024	Strong transcription Transcr. at gene 5' and 3' Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7101788	CDKN1C	cis	lymphoblastoid	seeQTL
rs7101788	SLC22A18AS	cis	cerebellum	SCAN
rs7101788	TRIM22	cis	cerebellum	SCAN
rs7101788	OR56A5	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:3830600-3861000	Weak transcription	Fetal Kidney	kidney
2	chr11:3844000-3857000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr11:3844400-3856200	Strong transcription	Fetal Stomach	stomach
4	chr11:3844800-3857000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:3845000-3856000	Weak transcription	HUVEC	blood vessel
6	chr11:3845200-3855800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr11:3845400-3855800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr11:3845600-3855800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr11:3848400-3861000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr11:3848600-3858200	Weak transcription	NHDF-Ad	bronchial
11	chr11:3849400-3855800	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr11:3849400-3855800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr11:3849400-3856000	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr11:3849400-3856000	Weak transcription	Brain Germinal Matrix	brain
15	chr11:3849400-3859000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr11:3849600-3855800	Weak transcription	Aorta	Aorta
17	chr11:3849600-3856400	Weak transcription	Ovary	ovary
18	chr11:3849600-3861000	Weak transcription	HSMMtube	muscle
19	chr11:3849800-3855800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr11:3849800-3856200	Weak transcription	HSMM	muscle
21	chr11:3851600-3856000	Weak transcription	NH-A	brain
22	chr11:3851600-3857200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr11:3851800-3856000	Weak transcription	Fetal Lung	lung
24	chr11:3852000-3855800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr11:3852000-3856000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr11:3852000-3856000	Enhancers	Brain Substantia Nigra	brain
27	chr11:3852000-3856600	Genic enhancers	Primary B cells from peripheral blood	blood
28	chr11:3852000-3858600	Enhancers	Brain Anterior Caudate	brain
29	chr11:3852200-3856200	Enhancers	Skeletal Muscle Male	skeletal muscle
30	chr11:3852200-3857000	Genic enhancers	Spleen	Spleen
31	chr11:3852200-3859800	Enhancers	Right Ventricle	heart
32	chr11:3852200-3860800	Enhancers	Small Intestine	intestine
33	chr11:3852400-3855800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr11:3852400-3856000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr11:3852400-3856000	Weak transcription	Osteobl	bone
36	chr11:3852400-3857200	Genic enhancers	Fetal Thymus	thymus
37	chr11:3852400-3859800	Weak transcription	Fetal Brain Female	brain
38	chr11:3852600-3856000	Enhancers	Pancreas	Pancrea
39	chr11:3852600-3857800	Transcr. at gene 5' and 3'	K562	blood
40	chr11:3852600-3860400	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
41	chr11:3852800-3855800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr11:3852800-3855800	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr11:3852800-3856800	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr11:3853000-3855800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr11:3853000-3858200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr11:3853000-3858200	Enhancers	Brain Cingulate Gyrus	brain
47	chr11:3853200-3855800	Enhancers	Sigmoid Colon	Sigmoid Colon
48	chr11:3853200-3856400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr11:3853400-3855800	Weak transcription	Esophagus	oesophagus
50	chr11:3853600-3855800	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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