Variant report

Variant	rs59530761
Chromosome Location	chr1:9906934-9906935
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	RAD21	chr1:9906703-9907160	ECC-1	luminal epithelium:	n/a	n/a
2	CTCF	chr1:9906820-9906970	HCPEpiC	choroid plexus:	n/a	n/a
3	CTCF	chr1:9906852-9906943	K562	blood:	n/a	n/a
4	UBTF	chr1:9906855-9906999	K562	blood:	n/a	n/a
5	CTCF	chr1:9906820-9906970	HBMEC	blood vessel:	n/a	n/a
6	POLR2A	chr1:9906831-9907685	K562	blood:	n/a	n/a
7	POLR2A	chr1:9906850-9907083	HepG2	liver:	n/a	n/a
8	EP300	chr1:9906515-9907278	ECC-1	luminal epithelium:	n/a	chr1:9906847-9906863
9	TCF12	chr1:9906683-9907308	ECC-1	luminal epithelium:	n/a	n/a
10	ZBTB7A	chr1:9906488-9907321	ECC-1	luminal epithelium:	n/a	n/a
11	ZBTB7A	chr1:9906726-9906986	K562	blood:	n/a	n/a
12	CTCF	chr1:9906682-9907023	K562	blood:	n/a	chr1:9906729-9906737
13	NFIC	chr1:9906637-9907399	ECC-1	luminal epithelium:	n/a	n/a
14	CTCF	chr1:9906675-9907058	K562	blood:	n/a	chr1:9906729-9906737
15	CTCF	chr1:9906800-9906950	AG04449	skin:	n/a	n/a
16	CTCF	chr1:9906820-9906970	WERI-Rb-1	eye:	n/a	n/a
17	JUND	chr1:9906901-9907060	H1-hESC	embryonic stem cell:	n/a	n/a
18	FOSL2	chr1:9906744-9907022	HepG2	liver:	n/a	chr1:9906774-9906783
19	POLR2A	chr1:9906724-9907115	H1-hESC	embryonic stem cell:	n/a	n/a
20	ZBTB7A	chr1:9906412-9907218	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:9882501..9887964-chr1:9906388..9911794,10	MCF-7	breast:
2	chr1:9897834..9901642-chr1:9903585..9906973,5	K562	blood:

Variant related genes	Relation type
ENSG00000223989	TF binding region
ENSG00000171603	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11121499	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11809921	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1220408	0.83[ASN][1000 genomes]
rs15177	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17034420	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2033960	0.86[EUR][1000 genomes]
rs2278611	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3860318	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3888014	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56315207	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57979292	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58281392	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59341676	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59533551	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60389428	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60547803	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60624175	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61785229	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61785586	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61785590	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6658583	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6683824	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6695334	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72858068	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7533225	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription 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	549 gene(s)	inside rSNPs	diseases
2	nsv871610	chr1:9655795-10008221	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv3372906	chr1:9838995-10052992	Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer 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	35 gene(s)	inside rSNPs	diseases
5	nsv871146	chr1:9897001-9951288	Genic enhancers Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9896000-9919200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr1:9896400-9908800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr1:9896600-9913400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:9901800-9907600	Enhancers	Fetal Muscle Leg	muscle
5	chr1:9901800-9908400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:9902000-9908600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:9902200-9908400	Weak transcription	Spleen	Spleen
8	chr1:9902200-9909800	Enhancers	Fetal Thymus	thymus
9	chr1:9902600-9911800	Weak transcription	HSMM	muscle
10	chr1:9902800-9907400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:9902800-9913600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:9903000-9908200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:9903200-9912200	Weak transcription	HSMMtube	muscle
14	chr1:9904000-9909400	Weak transcription	Gastric	stomach
15	chr1:9904000-9909800	Weak transcription	HepG2	liver
16	chr1:9904000-9913000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr1:9904000-9929800	Weak transcription	Aorta	Aorta
18	chr1:9904200-9908000	Weak transcription	Fetal Intestine Large	intestine
19	chr1:9904200-9910400	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr1:9904200-9912400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:9904200-9927400	Weak transcription	Colonic Mucosa	Colon
22	chr1:9904200-9927800	Weak transcription	Colon Smooth Muscle	Colon
23	chr1:9904400-9907800	Weak transcription	Fetal Intestine Small	intestine
24	chr1:9904400-9908000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:9904400-9909200	Weak transcription	Stomach Smooth Muscle	stomach
26	chr1:9904400-9909400	Weak transcription	Brain Germinal Matrix	brain
27	chr1:9904400-9911800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr1:9904400-9913400	Weak transcription	Fetal Lung	lung
29	chr1:9904400-9922600	Weak transcription	Pancreas	Pancrea
30	chr1:9904400-9923400	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr1:9904400-9927800	Weak transcription	Stomach Mucosa	stomach
32	chr1:9904400-9930000	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr1:9904600-9922600	Weak transcription	Ovary	ovary
34	chr1:9904600-9935000	Weak transcription	Osteobl	bone
35	chr1:9904800-9907200	Weak transcription	Fetal Heart	heart
36	chr1:9904800-9908800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr1:9904800-9910800	Weak transcription	Fetal Brain Female	brain
38	chr1:9904800-9946000	Weak transcription	Fetal Kidney	kidney
39	chr1:9905000-9908000	Weak transcription	Right Atrium	heart
40	chr1:9905000-9908200	Weak transcription	Fetal Stomach	stomach
41	chr1:9905000-9909600	Weak transcription	Fetal Brain Male	brain
42	chr1:9905000-9911800	Weak transcription	HMEC	breast
43	chr1:9905200-9907000	Weak transcription	Brain Angular Gyrus	brain
44	chr1:9905200-9908400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr1:9905200-9915400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr1:9905400-9908800	Enhancers	K562	blood
47	chr1:9905600-9909200	Weak transcription	NHLF	lung
48	chr1:9905600-9909600	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr1:9905800-9907000	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr1:9905800-9907400	Enhancers	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links