Variant report

Variant	rs9660699
Chromosome Location	chr1:46637840-46637841
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:66)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:66 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXM1	chr1:46636779-46637972	ECC-1	luminal epithelium:	n/a	n/a
2	CTCF	chr1:46637721-46637935	MCF-7	breast:	n/a	n/a
3	E2F6	chr1:46637346-46637954	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr1:46637799-46637874	LNCaP	prostate:	n/a	n/a
5	POLR2A	chr1:46637392-46637900	MCF-7	breast:	n/a	n/a
6	RAD21	chr1:46637406-46638207	MCF-7	breast:	n/a	n/a
7	MYC	chr1:46637498-46638003	MCF-7	breast:	n/a	n/a
8	TCF12	chr1:46637434-46638474	MCF-7	breast:	n/a	n/a
9	TFAP2C	chr1:46636896-46637939	Hela-S3	cervix:	n/a	chr1:46637178-46637187 chr1:46637703-46637718 chr1:46637744-46637759
10	SIN3AK20	chr1:46637103-46638506	MCF-7	breast:	n/a	n/a
11	NFIC	chr1:46636691-46638495	ECC-1	luminal epithelium:	n/a	n/a
12	ZBTB7A	chr1:46636924-46637976	ECC-1	luminal epithelium:	n/a	n/a
13	MAX	chr1:46636882-46638504	ECC-1	luminal epithelium:	n/a	n/a
14	MAX	chr1:46637505-46637994	H1-hESC	embryonic stem cell:	n/a	n/a
15	ZNF217	chr1:46637542-46638303	MCF-7	breast:	n/a	n/a
16	FOXA1	chr1:46637552-46637853	T-47D	breast:	n/a	n/a
17	TCF12	chr1:46636735-46638519	ECC-1	luminal epithelium:	n/a	n/a
18	MAX	chr1:46636899-46638460	ECC-1	luminal epithelium:	n/a	n/a
19	EP300	chr1:46637441-46637987	T-47D	breast:	n/a	chr1:46637847-46637856
20	MAX	chr1:46637380-46638132	HCT-116	colon:	n/a	n/a
21	EP300	chr1:46636699-46638570	ECC-1	luminal epithelium:	n/a	chr1:46637847-46637856 chr1:46637179-46637186
22	MAX	chr1:46637454-46638399	MCF-7	breast:	n/a	n/a
23	ELF1	chr1:46636896-46638388	MCF-7	breast:	n/a	n/a
24	EP300	chr1:46637471-46637972	T-47D	breast:	n/a	chr1:46637847-46637856
25	POLR2A	chr1:46636891-46638368	ECC-1	luminal epithelium:	n/a	n/a
26	YY1	chr1:46637459-46638006	ECC-1	luminal epithelium:	n/a	n/a
27	NR2F2	chr1:46636897-46638501	MCF-7	breast:	n/a	n/a
28	ELF1	chr1:46636909-46638107	MCF-7	breast:	n/a	n/a
29	NR2F2	chr1:46636996-46638347	MCF-7	breast:	n/a	n/a
30	ESR1	chr1:46637501-46637947	ECC-1	luminal epithelium:	n/a	n/a
31	TCF12	chr1:46637356-46638706	MCF-7	breast:	n/a	n/a
32	EP300	chr1:46637527-46638473	MCF-7	breast:	n/a	chr1:46637847-46637856
33	YY1	chr1:46637469-46637993	ECC-1	luminal epithelium:	n/a	n/a
34	HDAC2	chr1:46637390-46637994	MCF-7	breast:	n/a	chr1:46637643-46637651
35	ESR1	chr1:46636955-46637992	ECC-1	luminal epithelium:	n/a	n/a
36	CTCF	chr1:46637721-46637936	MCF-7	breast:	n/a	n/a
37	CTCF	chr1:46637737-46637936	MCF-7	breast:	n/a	n/a
38	ZBTB7A	chr1:46636848-46638085	ECC-1	luminal epithelium:	n/a	n/a
39	GABPA	chr1:46636722-46638105	MCF-7	breast:	n/a	n/a
40	GATA3	chr1:46637027-46638477	MCF-7	breast:	n/a	chr1:46637353-46637362
41	RAD21	chr1:46636858-46638424	ECC-1	luminal epithelium:	n/a	n/a
42	MYC	chr1:46637535-46637914	MCF-7	breast:	n/a	n/a
43	MYC	chr1:46637513-46638009	MCF-7	breast:	n/a	n/a
44	POLR2A	chr1:46637080-46638101	MCF-7	breast:	n/a	n/a
45	HA-E2F1	chr1:46637432-46638212	MCF-7	breast:	n/a	n/a
46	CTCF	chr1:46637730-46637930	MCF-7	breast:	n/a	n/a
47	CTCF	chr1:46637745-46637916	MCF-7	breast:	n/a	n/a
48	MYC	chr1:46637587-46637894	MCF-7	breast:	n/a	n/a
49	POLR2A	chr1:46636991-46637902	ECC-1	luminal epithelium:	n/a	n/a
50	E2F6	chr1:46637595-46637964	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:46593944..46606364-chr1:46632700..46654752,92	MCF-7	breast:
2	chr1:46636028..46638246-chr1:46712360..46714250,2	MCF-7	breast:
3	chr1:46636993..46639249-chr1:46644481..46646542,2	MCF-7	breast:
4	chr1:46636439..46638004-chr1:46642025..46643835,2	MCF-7	breast:
5	chr1:46636697..46639165-chr1:46652056..46653716,2	MCF-7	breast:
6	chr1:46635707..46641847-chr1:46658318..46665376,6	K562	blood:
7	chr1:46546706..46549522-chr1:46637741..46639306,2	MCF-7	breast:
8	chr1:46501344..46502975-chr1:46637425..46639494,2	MCF-7	breast:
9	chr1:46636220..46637897-chr1:46645659..46648862,3	MCF-7	breast:
10	chr1:46619572..46621835-chr1:46635358..46637893,2	MCF-7	breast:
11	chr1:46636119..46638195-chr2:81815588..81817410,2	MCF-7	breast:
12	chr1:46590920..46606215-chr1:46630948..46642525,66	MCF-7	breast:
13	chr1:46630846..46632404-chr1:46635981..46638710,2	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-POMGNT1-3	chr1:46637779-46637988	NONHSAT002987

No data

Variant related genes	Relation type
TSPAN1	TF binding region
ENSG00000117461	Chromatin interaction
ENSG00000085998	Chromatin interaction
ENSG00000250719	Chromatin interaction
ENSG00000085999	Chromatin interaction
ENSG00000227857	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12123115	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12131635	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55884940	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59843477	0.84[ASN][1000 genomes]
rs60794562	0.84[ASN][1000 genomes]
rs72677567	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7519183	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
2	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
3	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
4	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
5	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
6	nsv1006747	chr1:46476089-46655484	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv534947	chr1:46476089-46655484	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv1006530	chr1:46544842-46655484	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
9	nsv534949	chr1:46544842-46655484	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9660699	NSUN4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46633400-46638800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr1:46633400-46638800	Weak transcription	Brain Anterior Caudate	brain
3	chr1:46633400-46638800	Weak transcription	Colon Smooth Muscle	Colon
4	chr1:46633400-46638800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr1:46633600-46639200	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr1:46634400-46638800	Weak transcription	K562	blood
7	chr1:46635600-46642200	Enhancers	Lung	lung
8	chr1:46636600-46638000	Enhancers	HMEC	breast
9	chr1:46636800-46638000	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr1:46636800-46638000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:46636800-46638000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:46636800-46638000	Enhancers	Fetal Lung	lung
13	chr1:46636800-46638000	Enhancers	Gastric	stomach
14	chr1:46636800-46638000	Enhancers	Stomach Mucosa	stomach
15	chr1:46636800-46638000	Enhancers	Spleen	Spleen
16	chr1:46636800-46638200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr1:46636800-46638200	Enhancers	Primary B cells from peripheral blood	blood
18	chr1:46636800-46639400	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr1:46636800-46641200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:46636800-46641400	Enhancers	Placenta	Placenta
21	chr1:46636800-46642200	Enhancers	Left Ventricle	heart
22	chr1:46636800-46642400	Enhancers	Right Atrium	heart
23	chr1:46636800-46642400	Enhancers	Right Ventricle	heart
24	chr1:46637000-46638000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:46637000-46638000	Enhancers	Esophagus	oesophagus
26	chr1:46637000-46638000	Enhancers	Placenta Amnion	Placenta Amnion
27	chr1:46637000-46638000	Enhancers	NHEK	skin
28	chr1:46637000-46638200	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr1:46637000-46638200	Enhancers	Pancreas	Pancrea
30	chr1:46637000-46638600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr1:46637000-46641200	Enhancers	Fetal Muscle Leg	muscle
32	chr1:46637200-46638000	Enhancers	H1 Cell Line	embryonic stem cell
33	chr1:46637200-46638000	Enhancers	Colonic Mucosa	Colon
34	chr1:46637200-46638000	Enhancers	Rectal Mucosa Donor 29	rectum
35	chr1:46637200-46638000	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr1:46637200-46639800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr1:46637400-46638000	Enhancers	Fetal Muscle Trunk	muscle
38	chr1:46637400-46638800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr1:46637400-46638800	Weak transcription	Osteobl	bone
40	chr1:46637400-46639000	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr1:46637400-46639000	Weak transcription	GM12878-XiMat	blood
42	chr1:46637400-46639200	Weak transcription	HSMM	muscle
43	chr1:46637600-46638000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr1:46637600-46638000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr1:46637600-46638000	Enhancers	Psoas Muscle	Psoas
46	chr1:46637600-46639000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr1:46637800-46638400	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr1:46637800-46638800	Weak transcription	Brain Cingulate Gyrus	brain
49	chr1:46637800-46638800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr1:46637800-46638800	Enhancers	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links