Variant report

Variant	rs1790353
Chromosome Location	chr11:71136730-71136731
allele	A/G
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	CTCF	chr11:71136620-71136770	BE2_C	brain:	n/a	chr11:71136674-71136683 chr11:71136674-71136687
2	SMC3	chr11:71136539-71136767	HepG2	liver:	n/a	n/a
3	SIN3AK20	chr11:71136424-71137538	MCF-7	breast:	n/a	n/a
4	CTCF	chr11:71136580-71136730	MCF-7	breast:	n/a	chr11:71136674-71136683 chr11:71136674-71136687
5	CTCF	chr11:71136620-71136890	GM12873	blood:	n/a	chr11:71136674-71136683 chr11:71136797-71136810 chr11:71136674-71136687
6	CTCF	chr11:71136620-71136770	HAc	cerebellar:	n/a	chr11:71136674-71136683 chr11:71136674-71136687
7	CTCF	chr11:71136620-71136770	GM12868	blood:	n/a	chr11:71136674-71136683 chr11:71136674-71136687
8	RAD21	chr11:71136581-71136775	HepG2	liver:	n/a	chr11:71136675-71136688
9	CTCF	chr11:71136620-71136770	HFF-Myc	foreskin:	n/a	chr11:71136674-71136683 chr11:71136674-71136687
10	GATA3	chr11:71136728-71137155	T-47D	breast:	n/a	n/a
11	CTCF	chr11:71136640-71136790	GM12874	blood:	n/a	chr11:71136674-71136683 chr11:71136674-71136687
12	CTCF	chr11:71136620-71136770	HPF	lung:	n/a	chr11:71136674-71136683 chr11:71136674-71136687
13	CTCF	chr11:71136580-71136730	K562	blood:	n/a	chr11:71136674-71136683 chr11:71136674-71136687
14	HDAC2	chr11:71136656-71137376	MCF-7	breast:	n/a	chr11:71136916-71136930
15	CTCF	chr11:71136600-71136750	HRPEpiC	eye:	n/a	chr11:71136674-71136683 chr11:71136674-71136687
16	GATA3	chr11:71136722-71137390	MCF-7	breast:	n/a	n/a
17	CTCF	chr11:71136580-71136730	NHDF-neo	bronchial:	n/a	chr11:71136674-71136683 chr11:71136674-71136687
18	FOSL2	chr11:71136675-71137258	MCF-7	breast:	n/a	n/a
19	CTCF	chr11:71136580-71136730	GM12864	blood:	n/a	chr11:71136674-71136683 chr11:71136674-71136687
20	CTCF	chr11:71136640-71136790	HBMEC	blood vessel:	n/a	chr11:71136674-71136683 chr11:71136674-71136687
21	CTCF	chr11:71136620-71136770	HEK293	kidney:	n/a	chr11:71136674-71136683 chr11:71136674-71136687
22	ZNF217	chr11:71136682-71137232	MCF-7	breast:	n/a	n/a
23	CTCF	chr11:71136600-71136750	SK-N-SH_RA	brain:	n/a	chr11:71136674-71136683 chr11:71136674-71136687
24	CTCF	chr11:71136580-71136730	HA-sp	spinal cord:	n/a	chr11:71136674-71136683 chr11:71136674-71136687
25	CTCF	chr11:71136580-71136730	HEK293	kidney:	n/a	chr11:71136674-71136683 chr11:71136674-71136687
26	CTCF	chr11:71136600-71136750	GM12870	blood:	n/a	chr11:71136674-71136683 chr11:71136674-71136687
27	CTCF	chr11:71136500-71136790	HRPEpiC	eye:	n/a	chr11:71136674-71136683 chr11:71136674-71136687
28	MAX	chr11:71136393-71137436	MCF-7	breast:	n/a	n/a
29	FOSL1	chr11:71136678-71137331	HCT-116	colon:	n/a	n/a
30	CTCF	chr11:71136548-71136741	HepG2	liver:	n/a	chr11:71136674-71136683 chr11:71136674-71136687
31	CTCF	chr11:71136620-71136770	WERI-Rb-1	eye:	n/a	chr11:71136674-71136683 chr11:71136674-71136687
32	FOSL2	chr11:71136433-71137322	MCF-7	breast:	n/a	n/a
33	CTCF	chr11:71136600-71136750	HRE	kidney:	n/a	chr11:71136674-71136683 chr11:71136674-71136687
34	SIN3AK20	chr11:71136604-71137474	MCF-7	breast:	n/a	n/a
35	CTCF	chr11:71136580-71136730	A549	lung:	n/a	chr11:71136674-71136683 chr11:71136674-71136687
36	CTCF	chr11:71136660-71136810	GM12871	blood:	n/a	chr11:71136674-71136683 chr11:71136797-71136810 chr11:71136674-71136687
37	CTCF	chr11:71136580-71136731	K562	blood:	n/a	chr11:71136674-71136683 chr11:71136674-71136687
38	GATA3	chr11:71136716-71137198	T-47D	breast:	n/a	n/a
39	CTCF	chr11:71136620-71136770	A549	lung:	n/a	chr11:71136674-71136683 chr11:71136674-71136687
40	CTCF	chr11:71136620-71136770	HPAF	blood vessel:	n/a	chr11:71136674-71136683 chr11:71136674-71136687
41	CTCF	chr11:71136600-71136750	HUVEC	blood vessel:	n/a	chr11:71136674-71136683 chr11:71136674-71136687
42	CTCF	chr11:71136680-71136830	GM06990	blood:	n/a	chr11:71136797-71136810
43	CTCF	chr11:71136580-71136730	NB4	blood:	n/a	chr11:71136674-71136683 chr11:71136674-71136687
44	CTCF	chr11:71136580-71136730	GM12872	blood:	n/a	chr11:71136674-71136683 chr11:71136674-71136687
45	GATA3	chr11:71136494-71137535	MCF-7	breast:	n/a	n/a
46	CTCF	chr11:71136580-71136730	HMF	breast:	n/a	chr11:71136674-71136683 chr11:71136674-71136687
47	CTCF	chr11:71136640-71136790	GM12873	blood:	n/a	chr11:71136674-71136683 chr11:71136674-71136687
48	CTCF	chr11:71136580-71136730	GM12875	blood:	n/a	chr11:71136674-71136683 chr11:71136674-71136687
49	HDAC2	chr11:71136582-71137334	MCF-7	breast:	n/a	chr11:71136916-71136930
50	TCF12	chr11:71136689-71137251	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:71124009..71126373-chr11:71135133..71137138,2	K562	blood:
2	chr11:71122603..71125509-chr11:71135103..71137138,2	K562	blood:
3	chr11:71130483..71134539-chr11:71135016..71139274,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172900	TF binding region
ENSG00000172900	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10898144	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1123007	0.84[ASN][1000 genomes]
rs12224205	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1540127	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1619577	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1629220	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1630498	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1790324	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1790328	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1790330	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1790339	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1790340	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1790341	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1790343	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1790344	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1790345	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1790350	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1792224	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1792226	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1792227	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1792229	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1792231	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1792233	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1792234	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1792235	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1792264	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1792277	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1792280	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1792281	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1792282	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1792283	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1792284	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1792315	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1894100	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2002064	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2017686	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2276358	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2511010	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3794057	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4402322	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4435028	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4616066	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs736894	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1048123	chr11:70795222-71231382	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
2	nsv526973	chr11:71088949-71215880	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv897897	chr11:71088949-71217571	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers 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	14 gene(s)	inside rSNPs	diseases
4	nsv530623	chr11:71088949-72020418	Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
5	nsv897898	chr11:71103143-71211654	Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
6	nsv519224	chr11:71108341-71215880	Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1790353	RP11-660L16.2	cis	Skin Sun Exposed Lower leg	GTEx
rs1790353	RP11-660L16.2	cis	Thyroid	GTEx
rs1790353	NADSYN1	cis	Nerve Tibial	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:71123600-71139600	Weak transcription	Right Atrium	heart
2	chr11:71132600-71144000	Weak transcription	Spleen	Spleen
3	chr11:71135000-71150600	Weak transcription	NH-A	brain
4	chr11:71135400-71136800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr11:71135400-71136800	Weak transcription	Primary B cells from peripheral blood	blood
6	chr11:71135400-71137000	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr11:71135400-71139600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr11:71135400-71145000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr11:71136400-71137800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr11:71136400-71138000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr11:71136400-71138000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr11:71136400-71138000	Enhancers	HMEC	breast
13	chr11:71136600-71137000	Enhancers	Stomach Mucosa	stomach
14	chr11:71136600-71137200	Enhancers	Hela-S3	cervix
15	chr11:71136600-71137400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr11:71136600-71137800	Enhancers	GM12878-XiMat	blood
17	chr11:71136600-71137800	Enhancers	NHEK	skin

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