Variant report

Variant	rs6760065
Chromosome Location	chr2:99486318-99486319
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	ELF1	chr2:99485380-99486856	MCF-7	breast:	n/a	chr2:99485849-99485862 chr2:99485850-99485861 chr2:99485851-99485860
2	POLR2A	chr2:99485671-99486713	Hela-S3	cervix:	n/a	n/a
3	GTF2F1	chr2:99485663-99486572	Hela-S3	cervix:	n/a	n/a
4	USF1	chr2:99485823-99486723	ECC-1	luminal epithelium:	n/a	n/a
5	TCF12	chr2:99485559-99486800	ECC-1	luminal epithelium:	n/a	chr2:99486350-99486360
6	CTCF	chr2:99486280-99486430	SAEC	small airway:	n/a	n/a
7	MAX	chr2:99485624-99486876	MCF-7	breast:	n/a	chr2:99486481-99486492 chr2:99486482-99486491
8	POLR2A	chr2:99486186-99486732	ECC-1	luminal epithelium:	n/a	n/a
9	CTCF	chr2:99486240-99486390	NHEK	skin:	n/a	n/a
10	TCF7L2	chr2:99485733-99486703	Hela-S3	cervix:	n/a	n/a
11	MAX	chr2:99485646-99486771	ECC-1	luminal epithelium:	n/a	chr2:99486481-99486492 chr2:99486482-99486491
12	MAX	chr2:99485634-99486649	Hela-S3	cervix:	n/a	chr2:99486481-99486492 chr2:99486482-99486491
13	EP300	chr2:99485677-99486844	ECC-1	luminal epithelium:	n/a	chr2:99485745-99485754 chr2:99486240-99486254
14	RFX5	chr2:99485476-99486905	Hela-S3	cervix:	n/a	chr2:99486633-99486641
15	CEBPB	chr2:99486205-99486804	MCF-7	breast:	n/a	n/a
16	EP300	chr2:99486242-99486840	T-47D	breast:	n/a	n/a
17	RFX5	chr2:99486226-99487287	SK-N-SH	brain:	n/a	chr2:99487133-99487142 chr2:99486633-99486641
18	HDAC2	chr2:99485396-99486857	MCF-7	breast:	n/a	n/a
19	GATA3	chr2:99486234-99486766	T-47D	breast:	n/a	chr2:99486511-99486523
20	EP300	chr2:99486308-99486681	T-47D	breast:	n/a	n/a
21	MAX	chr2:99485535-99486886	ECC-1	luminal epithelium:	n/a	chr2:99486481-99486492 chr2:99486482-99486491
22	NFIC	chr2:99485582-99486976	ECC-1	luminal epithelium:	n/a	chr2:99486601-99486629
23	RUNX3	chr2:99486126-99486451	GM12878	blood:	n/a	n/a
24	FOXA1	chr2:99486302-99486802	T-47D	breast:	n/a	n/a
25	ELF1	chr2:99485342-99486765	MCF-7	breast:	n/a	chr2:99485849-99485862 chr2:99485850-99485861 chr2:99485851-99485860
26	CTCF	chr2:99486280-99486430	MCF-7	breast:	n/a	n/a
27	RCOR1	chr2:99485643-99486622	Hela-S3	cervix:	n/a	n/a
28	USF2	chr2:99485947-99486771	Hela-S3	cervix:	n/a	chr2:99486481-99486492
29	CTCF	chr2:99486280-99486430	HMEC	breast:	n/a	n/a
30	CEBPB	chr2:99485730-99486741	Hela-S3	cervix:	n/a	n/a
31	CTCF	chr2:99486200-99486350	Hela-S3	cervix:	n/a	n/a
32	CTCF	chr2:99486180-99486330	NHEK	skin:	n/a	n/a
33	CTCF	chr2:99486260-99486410	MCF-7	breast:	n/a	n/a
34	SMC3	chr2:99485853-99486559	Hela-S3	cervix:	n/a	chr2:99486144-99486154 chr2:99486505-99486512
35	MAX	chr2:99485372-99486841	MCF-7	breast:	n/a	chr2:99486481-99486492 chr2:99486482-99486491
36	GATA3	chr2:99486317-99486718	MCF-7	breast:	n/a	chr2:99486511-99486523
37	TFAP2A	chr2:99485440-99486459	Hela-S3	cervix:	n/a	n/a
38	TEAD4	chr2:99485563-99486816	ECC-1	luminal epithelium:	n/a	n/a
39	USF1	chr2:99486115-99486830	ECC-1	luminal epithelium:	n/a	n/a
40	NFIC	chr2:99485503-99486914	ECC-1	luminal epithelium:	n/a	chr2:99486601-99486629
41	NR2F2	chr2:99485561-99486818	MCF-7	breast:	n/a	n/a
42	GATA3	chr2:99486242-99486767	T-47D	breast:	n/a	chr2:99486511-99486523
43	SRF	chr2:99485718-99486801	MCF-7	breast:	n/a	chr2:99486140-99486150
44	GATA3	chr2:99485440-99486871	MCF-7	breast:	n/a	chr2:99486511-99486523
45	SIN3AK20	chr2:99484869-99487036	MCF-7	breast:	n/a	n/a
46	GATA3	chr2:99485632-99486870	MCF-7	breast:	n/a	chr2:99486511-99486523
47	TCF12	chr2:99485436-99486934	ECC-1	luminal epithelium:	n/a	chr2:99486350-99486360
48	TFAP2C	chr2:99485377-99486572	Hela-S3	cervix:	n/a	n/a
49	ZNF217	chr2:99485484-99486759	MCF-7	breast:	n/a	n/a
50	NR2F2	chr2:99484910-99486778	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:99223862..99225617-chr2:99483733..99486358,2	MCF-7	breast:
2	chr2:99485026..99487433-chr2:100105196..100107704,3	MCF-7	breast:
3	chr2:99484412..99487919-chr2:99523957..99528531,6	MCF-7	breast:

Variant related genes	Relation type
KIAA1211L	TF binding region
ENSG00000115446	Chromatin interaction
ENSG00000183513	Chromatin interaction
ENSG00000135945	Chromatin interaction
ENSG00000196872	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10175560	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10192266	0.82[EUR][1000 genomes]
rs11123756	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11900176	0.84[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.90[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11900524	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12467504	0.84[EUR][1000 genomes]
rs12474283	0.84[CEU][hapmap]
rs12478574	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12712033	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs12712034	0.83[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12712037	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12712039	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12712040	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12712042	0.81[EUR][1000 genomes]
rs12990579	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13004700	0.84[CEU][hapmap]
rs13005124	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs13005148	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13006398	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13024838	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13028500	0.91[CEU][hapmap]
rs1581249	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17758170	0.96[CEU][hapmap];0.89[CHB][hapmap];0.90[GIH][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes]
rs1878589	0.96[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1949424	0.92[EUR][1000 genomes]
rs1962029	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2280142	0.85[MEX][hapmap]
rs4311103	0.88[CEU][hapmap]
rs4499468	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4553869	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4850890	0.81[EUR][1000 genomes]
rs4851174	0.86[CEU][hapmap];0.80[EUR][1000 genomes]
rs4851175	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs4851176	0.81[EUR][1000 genomes]
rs6542837	0.85[MEX][hapmap];0.80[EUR][1000 genomes]
rs6542839	0.83[GIH][hapmap]
rs6542841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6542845	0.81[EUR][1000 genomes]
rs6704682	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6724477	0.96[CEU][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs6739097	0.83[EUR][1000 genomes]
rs6741166	0.92[EUR][1000 genomes]
rs6742047	0.81[EUR][1000 genomes]
rs6752025	0.93[EUR][1000 genomes]
rs6755640	0.81[EUR][1000 genomes]
rs6757098	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7423519	0.96[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7565510	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7565614	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7565736	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7565819	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7588441	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7590596	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7593332	0.92[EUR][1000 genomes]
rs7608889	0.84[CEU][hapmap]
rs883773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs885115	0.81[EUR][1000 genomes]
rs925887	0.87[CEU][hapmap]

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	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv582517	chr2:99440917-99487972	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6760065	LIPT1	cis	parietal	SCAN
rs6760065	FAHD2B	cis	parietal	SCAN
rs6760065	TSGA10	cis	cerebellum	SCAN
rs6760065	LIPT1	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99481400-99486400	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr2:99481400-99486400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:99481800-99487000	Weak transcription	Lung	lung
4	chr2:99484000-99489000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr2:99484200-99486600	Flanking Active TSS	Hela-S3	cervix
6	chr2:99484600-99486400	Flanking Active TSS	NHEK	skin
7	chr2:99484800-99486400	Flanking Active TSS	Fetal Intestine Large	intestine
8	chr2:99485000-99486400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:99485000-99486400	Active TSS	Rectal Smooth Muscle	rectum
10	chr2:99485000-99486800	Active TSS	Duodenum Mucosa	Duodenum
11	chr2:99485000-99488200	Enhancers	Fetal Muscle Leg	muscle
12	chr2:99485200-99487400	Weak transcription	Brain Angular Gyrus	brain
13	chr2:99485200-99487800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr2:99485400-99486400	Enhancers	H1 Cell Line	embryonic stem cell
15	chr2:99485400-99486400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr2:99485400-99486400	Flanking Active TSS	Fetal Intestine Small	intestine
17	chr2:99485400-99486400	Active TSS	Gastric	stomach
18	chr2:99485400-99486600	Active TSS	Colonic Mucosa	Colon
19	chr2:99485400-99486600	Flanking Active TSS	Pancreas	Pancrea
20	chr2:99485400-99486800	Enhancers	Placenta	Placenta
21	chr2:99485400-99487400	Enhancers	Fetal Muscle Trunk	muscle
22	chr2:99485600-99486400	Active TSS	Stomach Mucosa	stomach
23	chr2:99485600-99499800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr2:99485800-99486600	Enhancers	Placenta Amnion	Placenta Amnion
25	chr2:99485800-99486800	Enhancers	GM12878-XiMat	blood
26	chr2:99485800-99487000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
27	chr2:99485800-99488200	Enhancers	Cortex derived primary cultured neurospheres	brain
28	chr2:99485800-99491800	Weak transcription	Brain Anterior Caudate	brain
29	chr2:99486000-99486400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
30	chr2:99486000-99486600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
31	chr2:99486000-99487600	Enhancers	Fetal Thymus	thymus
32	chr2:99486000-99488600	Weak transcription	Right Atrium	heart
33	chr2:99486200-99486400	Flanking Active TSS	Esophagus	oesophagus
34	chr2:99486200-99486400	Enhancers	HSMMtube	muscle
35	chr2:99486200-99486600	Active TSS	Primary T regulatory cells fromperipheralblood	blood
36	chr2:99486200-99486600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr2:99486200-99487000	Enhancers	HMEC	breast
38	chr2:99486200-99487600	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr2:99486200-99487800	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr2:99486200-99489800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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