Variant report

Variant	rs4141309
Chromosome Location	chr7:120498608-120498609
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	TBP	chr7:120497962-120498645	Hela-S3	cervix:	n/a	n/a
2	CEBPB	chr7:120497722-120498639	Hela-S3	cervix:	n/a	chr7:120498487-120498500
3	YY1	chr7:120498130-120498625	ECC-1	luminal epithelium:	n/a	chr7:120498156-120498170 chr7:120498157-120498171
4	ZNF384	chr7:120497652-120498720	K562	blood:	n/a	n/a
5	POLR2A	chr7:120497109-120498678	Hela-S3	cervix:	n/a	n/a
6	CTCF	chr7:120497493-120498624	SK-N-SH	brain:	n/a	chr7:120497812-120497825 chr7:120497726-120497739
7	MAZ	chr7:120497589-120498678	Hela-S3	cervix:	n/a	chr7:120498017-120498027 chr7:120497893-120497902
8	CHD2	chr7:120497596-120498647	Hela-S3	cervix:	n/a	chr7:120497739-120497749
9	POLR2A	chr7:120497577-120498617	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr7:120496079-120498638	GM12878	blood:	n/a	n/a
11	MAX	chr7:120497166-120498673	Hela-S3	cervix:	n/a	chr7:120498017-120498027 chr7:120497893-120497902
12	STAT3	chr7:120498418-120498618	MCF10A-Er-Src	breast:	n/a	n/a
13	MAX	chr7:120496770-120498657	HCT-116	colon:	n/a	chr7:120498017-120498027 chr7:120497893-120497902
14	BRCA1	chr7:120497835-120498612	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr7:120497356-120498615	H1-hESC	embryonic stem cell:	n/a	n/a
16	MAX	chr7:120497488-120498614	A549	lung:	n/a	chr7:120498017-120498027 chr7:120497893-120497902
17	CHD1	chr7:120498603-120498862	GM12878	blood:	n/a	n/a
18	RFX5	chr7:120497632-120498646	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr7:120497585-120498686	HEK293	kidney:	n/a	n/a
20	TCF7L2	chr7:120498354-120498828	HEK293	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:3072484..3075327-chr7:120496877..120499119,2	MCF-7	breast:
2	chr7:120495769..120499665-chr7:120588624..120592417,7	MCF-7	breast:

Variant related genes	Relation type
TSPAN12	TF binding region
ENSG00000071243	Chromatin interaction
ENSG00000103145	Chromatin interaction
ENSG00000131652	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10252911	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[CHD][hapmap]
rs10257297	0.81[ASN][1000 genomes]
rs10257475	0.81[ASN][1000 genomes]
rs10261886	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10272601	1.00[CEU][hapmap]
rs12154992	1.00[CEU][hapmap]
rs13438082	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17132716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs17143001	0.90[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs17143009	0.90[CHB][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs17143055	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1859316	1.00[CEU][hapmap];0.85[CHB][hapmap]
rs2107276	0.85[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs2158323	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2158324	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2189452	1.00[ASW][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.81[MEX][hapmap];0.82[MKK][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2402551	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2721341	0.83[CHD][hapmap]
rs3757556	1.00[CEU][hapmap]
rs3757557	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3779386	0.85[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs3779387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3779388	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs3779389	1.00[ASW][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.82[YRI][hapmap];0.82[ASN][1000 genomes]
rs3823859	0.83[CHD][hapmap]
rs4141301	1.00[CEU][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs4461820	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56755229	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs56922360	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57457261	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57816892	0.80[AFR][1000 genomes]
rs57818444	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs58686737	0.89[ASN][1000 genomes]
rs59169713	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59189516	0.89[AMR][1000 genomes]
rs59567952	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59790582	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs60612048	0.89[AMR][1000 genomes]
rs60837162	0.83[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs61043018	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6466762	0.82[CHD][hapmap]
rs6964344	1.00[CEU][hapmap];0.83[CHD][hapmap]
rs6971854	0.85[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs6975372	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6979247	1.00[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs714259	0.84[CHB][hapmap]
rs73427805	0.87[ASN][1000 genomes]
rs73427831	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73427834	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73427862	0.81[ASN][1000 genomes]
rs73429803	0.81[ASN][1000 genomes]
rs7776721	1.00[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs7779136	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7779149	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7779941	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7780130	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7780247	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7780690	0.85[AMR][1000 genomes]
rs7781985	0.85[CHD][hapmap]
rs7789807	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs7799562	0.85[AMR][1000 genomes]
rs7800318	0.87[ASN][1000 genomes]
rs7806629	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9648991	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9648992	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9648993	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9649427	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9649428	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9649429	0.81[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	esv1818826	chr7:120405335-120622836	Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv5929	chr7:120467591-120513472	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	esv3438279	chr7:120496341-120498889	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:120496000-120499000	Active TSS	Fetal Kidney	kidney
2	chr7:120496200-120498800	Active TSS	Aorta	Aorta
3	chr7:120496200-120498800	Active TSS	Colon Smooth Muscle	Colon
4	chr7:120496200-120499000	Active TSS	Right Ventricle	heart
5	chr7:120496400-120498800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr7:120496400-120498800	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr7:120496400-120498800	Active TSS	Stomach Smooth Muscle	stomach
8	chr7:120496600-120498800	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr7:120496600-120498800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr7:120496600-120498800	Active TSS	Brain Anterior Caudate	brain
11	chr7:120496600-120498800	Active TSS	Fetal Heart	heart
12	chr7:120496600-120498800	Active TSS	HSMMtube	muscle
13	chr7:120496600-120499000	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr7:120496800-120498800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr7:120496800-120498800	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr7:120497000-120498800	Active TSS	H1 Cell Line	embryonic stem cell
17	chr7:120497000-120498800	Active TSS	Brain Hippocampus Middle	brain
18	chr7:120497000-120498800	Active TSS	Fetal Intestine Large	intestine
19	chr7:120497000-120498800	Active TSS	Fetal Lung	lung
20	chr7:120497000-120498800	Active TSS	Fetal Muscle Leg	muscle
21	chr7:120497000-120498800	Active TSS	Fetal Stomach	stomach
22	chr7:120497000-120499000	Active TSS	Rectal Smooth Muscle	rectum
23	chr7:120497200-120498800	Active TSS	Brain Cingulate Gyrus	brain
24	chr7:120497200-120498800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr7:120497200-120498800	Active TSS	Brain Substantia Nigra	brain
26	chr7:120497200-120498800	Active TSS	Fetal Intestine Small	intestine
27	chr7:120497200-120498800	Active TSS	Skeletal Muscle Male	skeletal muscle
28	chr7:120497200-120499200	Active TSS	Rectal Mucosa Donor 31	rectum
29	chr7:120497400-120498800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
30	chr7:120497800-120498800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr7:120497800-120499000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr7:120498200-120498800	Flanking Active TSS	Adipose Nuclei	Adipose
33	chr7:120498400-120498800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
34	chr7:120498400-120498800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr7:120498400-120498800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr7:120498400-120498800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
37	chr7:120498400-120498800	Flanking Active TSS	HUVEC	blood vessel
38	chr7:120498400-120499000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr7:120498400-120499000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr7:120498400-120499000	Flanking Active TSS	Liver	Liver
41	chr7:120498400-120499000	Active TSS	Right Atrium	heart
42	chr7:120498400-120499000	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr7:120498400-120499200	Enhancers	Small Intestine	intestine
44	chr7:120498400-120499400	Bivalent/Poised TSS	Fetal Brain Male	brain
45	chr7:120498400-120504600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr7:120498400-120506800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr7:120498600-120498800	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr7:120498600-120498800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
49	chr7:120498600-120498800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
50	chr7:120498600-120498800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links