Variant report

Variant	rs12623171
Chromosome Location	chr2:99485920-99485921
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	POLR2A	chr2:99485424-99486309	Hela-S3	cervix:	n/a	n/a
6	TCF12	chr2:99485559-99486800	ECC-1	luminal epithelium:	n/a	chr2:99486350-99486360
7	POLR2A	chr2:99485534-99486172	MCF-7	breast:	n/a	n/a
8	FOS	chr2:99485780-99486133	MCF10A-Er-Src	breast:	n/a	chr2:99485928-99485937
9	MAX	chr2:99485624-99486876	MCF-7	breast:	n/a	chr2:99486481-99486492 chr2:99486482-99486491
10	GATA3	chr2:99485567-99486068	T-47D	breast:	n/a	n/a
11	TCF7L2	chr2:99485733-99486703	Hela-S3	cervix:	n/a	n/a
12	MAX	chr2:99485646-99486771	ECC-1	luminal epithelium:	n/a	chr2:99486481-99486492 chr2:99486482-99486491
13	FOS	chr2:99485824-99486120	MCF10A-Er-Src	breast:	n/a	chr2:99485928-99485937
14	MAX	chr2:99485634-99486649	Hela-S3	cervix:	n/a	chr2:99486481-99486492 chr2:99486482-99486491
15	EP300	chr2:99485677-99486844	ECC-1	luminal epithelium:	n/a	chr2:99485745-99485754 chr2:99486240-99486254
16	RFX5	chr2:99485476-99486905	Hela-S3	cervix:	n/a	chr2:99486633-99486641
17	FOXA2	chr2:99485844-99486074	HepG2	liver:	n/a	n/a
18	HDAC2	chr2:99485396-99486857	MCF-7	breast:	n/a	n/a
19	MAFK	chr2:99485834-99486034	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr2:99485550-99486040	ECC-1	luminal epithelium:	n/a	n/a
21	FOXA1	chr2:99485653-99486118	T-47D	breast:	n/a	n/a
22	ELF1	chr2:99485731-99486007	K562	blood:	n/a	chr2:99485849-99485862 chr2:99485850-99485861 chr2:99485851-99485860
23	CTCF	chr2:99485840-99485990	GM12867	blood:	n/a	n/a
24	POLR2A	chr2:99485457-99486101	MCF-7	breast:	n/a	n/a
25	ELF1	chr2:99485657-99485989	HepG2	liver:	n/a	chr2:99485849-99485862 chr2:99485850-99485861 chr2:99485851-99485860
26	MXI1	chr2:99485692-99486149	Hela-S3	cervix:	n/a	n/a
27	MAX	chr2:99485535-99486886	ECC-1	luminal epithelium:	n/a	chr2:99486481-99486492 chr2:99486482-99486491
28	MYC	chr2:99485746-99486039	MCF-7	breast:	n/a	n/a
29	NFIC	chr2:99485582-99486976	ECC-1	luminal epithelium:	n/a	chr2:99486601-99486629
30	ELF1	chr2:99485342-99486765	MCF-7	breast:	n/a	chr2:99485849-99485862 chr2:99485850-99485861 chr2:99485851-99485860
31	POLR2A	chr2:99485528-99486138	ECC-1	luminal epithelium:	n/a	n/a
32	RCOR1	chr2:99485643-99486622	Hela-S3	cervix:	n/a	n/a
33	FOXA1	chr2:99485679-99486147	T-47D	breast:	n/a	n/a
34	BRCA1	chr2:99485920-99486120	Hela-S3	cervix:	n/a	n/a
35	FOS	chr2:99485905-99486015	MCF10A-Er-Src	breast:	n/a	chr2:99485928-99485937
36	STAT3	chr2:99485826-99486225	MCF10A-Er-Src	breast:	n/a	n/a
37	CEBPB	chr2:99485730-99486741	Hela-S3	cervix:	n/a	n/a
38	ZKSCAN1	chr2:99485752-99486142	Hela-S3	cervix:	n/a	n/a
39	SMC3	chr2:99485853-99486559	Hela-S3	cervix:	n/a	chr2:99486144-99486154 chr2:99486505-99486512
40	MAX	chr2:99485372-99486841	MCF-7	breast:	n/a	chr2:99486481-99486492 chr2:99486482-99486491
41	ZNF143	chr2:99485643-99485954	Hela-S3	cervix:	n/a	n/a
42	TFAP2A	chr2:99485440-99486459	Hela-S3	cervix:	n/a	n/a
43	POLR2A	chr2:99485624-99485996	MCF10A-Er-Src	breast:	n/a	n/a
44	TBP	chr2:99485807-99486111	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr2:99485653-99485970	Hela-S3	cervix:	n/a	n/a
46	FOXA1	chr2:99485873-99486069	ECC-1	luminal epithelium:	n/a	n/a
47	CHD2	chr2:99485622-99486091	Hela-S3	cervix:	n/a	n/a
48	TEAD4	chr2:99485563-99486816	ECC-1	luminal epithelium:	n/a	n/a
49	NFIC	chr2:99485503-99486914	ECC-1	luminal epithelium:	n/a	chr2:99486601-99486629
50	MYC	chr2:99485730-99486179	MCF10A-Er-Src	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
ENSG00000196872	Chromatin interaction
ENSG00000135945	Chromatin interaction
ENSG00000115446	Chromatin interaction
ENSG00000183513	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12232948	1.00[CHB][hapmap]
rs12611969	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12612736	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12614153	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12615518	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12616060	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12616866	1.00[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12617554	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12619244	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12620812	1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12622254	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12622445	1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12623022	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12623172	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12623472	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17022063	1.00[YRI][hapmap]
rs35979410	1.00[CHB][hapmap];0.82[AMR][1000 genomes]
rs56943554	0.82[AMR][1000 genomes]
rs57480100	0.82[AMR][1000 genomes]
rs61419135	0.82[AMR][1000 genomes]
rs61552487	0.82[AMR][1000 genomes]
rs61604726	0.82[AMR][1000 genomes]
rs6760422	0.86[ASN][1000 genomes]
rs868921	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[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	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

No data

Chromatin state (count:42 , 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	chr2:99483000-99486000	Weak transcription	HSMM	muscle
5	chr2:99484000-99489000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr2:99484200-99486600	Flanking Active TSS	Hela-S3	cervix
7	chr2:99484600-99486200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:99484600-99486400	Flanking Active TSS	NHEK	skin
9	chr2:99484800-99486200	Active TSS	Esophagus	oesophagus
10	chr2:99484800-99486200	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr2:99484800-99486400	Flanking Active TSS	Fetal Intestine Large	intestine
12	chr2:99485000-99486000	Active TSS	Rectal Mucosa Donor 29	rectum
13	chr2:99485000-99486200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr2:99485000-99486200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr2:99485000-99486400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr2:99485000-99486400	Active TSS	Rectal Smooth Muscle	rectum
17	chr2:99485000-99486800	Active TSS	Duodenum Mucosa	Duodenum
18	chr2:99485000-99488200	Enhancers	Fetal Muscle Leg	muscle
19	chr2:99485200-99486000	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr2:99485200-99486200	Flanking Active TSS	HMEC	breast
21	chr2:99485200-99487400	Weak transcription	Brain Angular Gyrus	brain
22	chr2:99485200-99487800	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr2:99485400-99486000	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr2:99485400-99486200	Flanking Bivalent TSS/Enh	HepG2	liver
25	chr2:99485400-99486400	Enhancers	H1 Cell Line	embryonic stem cell
26	chr2:99485400-99486400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr2:99485400-99486400	Flanking Active TSS	Fetal Intestine Small	intestine
28	chr2:99485400-99486400	Active TSS	Gastric	stomach
29	chr2:99485400-99486600	Active TSS	Colonic Mucosa	Colon
30	chr2:99485400-99486600	Flanking Active TSS	Pancreas	Pancrea
31	chr2:99485400-99486800	Enhancers	Placenta	Placenta
32	chr2:99485400-99487400	Enhancers	Fetal Muscle Trunk	muscle
33	chr2:99485600-99486000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr2:99485600-99486000	Active TSS	Rectal Mucosa Donor 31	rectum
35	chr2:99485600-99486400	Active TSS	Stomach Mucosa	stomach
36	chr2:99485600-99499800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr2:99485800-99486200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
38	chr2:99485800-99486600	Enhancers	Placenta Amnion	Placenta Amnion
39	chr2:99485800-99486800	Enhancers	GM12878-XiMat	blood
40	chr2:99485800-99487000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
41	chr2:99485800-99488200	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr2:99485800-99491800	Weak transcription	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links