Variant report

Variant	rs13414407
Chromosome Location	chr2:234313158-234313159
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	STAT3	chr2:234312966-234313178	MCF10A-Er-Src	breast:	n/a	n/a
2	ZNF143	chr2:234312892-234313230	K562	blood:	n/a	n/a
3	CTCF	chr2:234312920-234313190	Hela-S3	cervix:	n/a	chr2:234313067-234313085
4	CTCF	chr2:234312945-234313178	MCF-7	breast:	n/a	chr2:234313067-234313085
5	JUND	chr2:234312960-234313165	K562	blood:	n/a	n/a
6	CTCF	chr2:234312808-234313335	MCF-7	breast:	n/a	chr2:234313067-234313085
7	CTCF	chr2:234313020-234313170	Caco-2	colon:	n/a	chr2:234313067-234313085
8	STAT1	chr2:234313005-234313179	GM12878	blood:	n/a	n/a
9	CTCF	chr2:234312941-234313303	K562	blood:	n/a	chr2:234313067-234313085
10	WRNIP1	chr2:234312934-234313219	GM12878	blood:	n/a	n/a
11	CTCF	chr2:234312956-234313373	HCT-116	colon:	n/a	chr2:234313067-234313085
12	CTCF	chr2:234313020-234313170	NHDF-neo	bronchial:	n/a	chr2:234313067-234313085
13	CTCF	chr2:234312919-234313209	GM19238	blood:	n/a	chr2:234313067-234313085
14	RAD21	chr2:234312836-234313321	HepG2	liver:	n/a	chr2:234313068-234313087
15	SMC3	chr2:234312900-234313254	K562	blood:	n/a	n/a
16	RAD21	chr2:234312920-234313187	GM12878	blood:	n/a	chr2:234313068-234313087
17	CTCF	chr2:234312903-234313260	H1-hESC	embryonic stem cell:	n/a	chr2:234313067-234313085
18	CTCF	chr2:234312842-234313273	K562	blood:	n/a	chr2:234313067-234313085
19	RAD21	chr2:234312784-234313451	SK-N-SH	brain:	n/a	chr2:234313068-234313087
20	CTCF	chr2:234312616-234313935	A549	lung:	n/a	chr2:234313067-234313085
21	CTCF	chr2:234312904-234313190	HepG2	liver:	n/a	chr2:234313067-234313085
22	YY1	chr2:234312955-234313184	GM12878	blood:	n/a	n/a
23	CTCF	chr2:234312947-234313174	Fibrobl	skin:	n/a	chr2:234313067-234313085
24	CTCF	chr2:234312923-234313186	ECC-1	luminal epithelium:	n/a	chr2:234313067-234313085
25	CTCF	chr2:234313020-234313170	GM12872	blood:	n/a	chr2:234313067-234313085
26	RAD21	chr2:234312797-234313384	A549	lung:	n/a	chr2:234313068-234313087
27	CTCF	chr2:234312928-234313200	NHEK	skin:	n/a	chr2:234313067-234313085
28	CTCF	chr2:234312959-234313189	Lung_OC	lung:	n/a	chr2:234313067-234313085
29	RAD21	chr2:234312706-234313482	HCT-116	colon:	n/a	chr2:234313068-234313087
30	CTCF	chr2:234312952-234313179	MCF-7	breast:	n/a	chr2:234313067-234313085
31	RAD21	chr2:234312797-234313479	HCT-116	colon:	n/a	chr2:234313068-234313087
32	SMC3	chr2:234312870-234313293	Hela-S3	cervix:	n/a	n/a
33	CTCF	chr2:234312979-234313168	GM13976	blood:	n/a	chr2:234313067-234313085
34	CTCF	chr2:234312834-234313211	A549	lung:	n/a	chr2:234313067-234313085
35	CTCF	chr2:234312937-234313188	GM19239	blood:	n/a	chr2:234313067-234313085
36	CTCF	chr2:234312930-234313204	MCF-7	breast:	n/a	chr2:234313067-234313085
37	CTCF	chr2:234312877-234313174	K562	blood:	n/a	chr2:234313067-234313085
38	CTCF	chr2:234313020-234313170	AG04450	lung:	n/a	chr2:234313067-234313085
39	CTCF	chr2:234312885-234313258	ECC-1	luminal epithelium:	n/a	chr2:234313067-234313085
40	RAD21	chr2:234312863-234313307	Hela-S3	cervix:	n/a	chr2:234313068-234313087
41	CTCF	chr2:234312685-234313487	HCT-116	colon:	n/a	chr2:234313067-234313085
42	CTCF	chr2:234312945-234313190	H1-hESC	embryonic stem cell:	n/a	chr2:234313067-234313085
43	RAD21	chr2:234312877-234313237	HepG2	liver:	n/a	chr2:234313068-234313087
44	CTCF	chr2:234312959-234313196	A549	lung:	n/a	chr2:234313067-234313085
45	RAD21	chr2:234312892-234313207	SK-N-SH_RA	brain:	n/a	chr2:234313068-234313087
46	CTCF	chr2:234312891-234313213	GM12878	blood:	n/a	chr2:234313067-234313085
47	RAD21	chr2:234312735-234313427	A549	lung:	n/a	chr2:234313068-234313087
48	CTCF	chr2:234312932-234313196	GM12892	blood:	n/a	chr2:234313067-234313085
49	CTCF	chr2:234312949-234313183	MCF-7	breast:	n/a	chr2:234313067-234313085
50	CTCF	chr2:234313020-234313170	HA-sp	spinal cord:	n/a	chr2:234313067-234313085

No.	Distal block	Cell Line	Cell type
1	chr2:234287251..234289856-chr2:234310620..234313418,2	MCF-7	breast:
2	chr2:234312047..234314446-chr2:234350667..234352511,2	MCF-7	breast:
3	chr2:234312601..234313556-chr2:234351945..234352727,3	MCF-7	breast:
4	chr2:234312633..234313516-chr2:234741267..234742065,2	MCF-7	breast:
5	chr2:234312176..234314651-chr2:234316905..234320514,3	MCF-7	breast:
6	chr2:234312603..234313536-chr2:234351871..234353115,15	MCF-7	breast:
7	chr2:234312613..234313597-chr2:234351835..234352949,7	K562	blood:
8	chr2:234313157..234314685-chr2:234334796..234337300,2	K562	blood:

Variant related genes	Relation type
DGKD	TF binding region
ENSG00000201013	Chromatin interaction
ENSG00000077044	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10168794	1.00[CEU][hapmap];0.94[YRI][hapmap]
rs10169180	1.00[CHB][hapmap]
rs10177761	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10178357	1.00[CHB][hapmap]
rs10181039	1.00[EUR][1000 genomes]
rs10183033	1.00[CHB][hapmap]
rs10185923	1.00[CHB][hapmap]
rs10193542	1.00[CEU][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10803653	1.00[CHB][hapmap]
rs10929195	1.00[CHB][hapmap]
rs1097930	1.00[CHB][hapmap]
rs1097931	1.00[CHB][hapmap]
rs11888993	0.85[EUR][1000 genomes]
rs11892545	1.00[CEU][hapmap];0.94[GIH][hapmap];0.83[TSI][hapmap];0.94[YRI][hapmap];0.93[EUR][1000 genomes]
rs1220430	1.00[CHB][hapmap]
rs12473824	1.00[CHB][hapmap]
rs12615446	1.00[CHB][hapmap]
rs13384932	1.00[CEU][hapmap]
rs13391864	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];0.82[JPT][hapmap];0.88[TSI][hapmap];0.94[YRI][hapmap];0.88[EUR][1000 genomes]
rs13392183	0.90[EUR][1000 genomes]
rs13400471	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs13400563	1.00[CEU][hapmap];0.94[YRI][hapmap];0.93[EUR][1000 genomes]
rs13403169	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes]
rs13406462	1.00[JPT][hapmap]
rs13406655	0.82[JPT][hapmap]
rs13419277	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13425849	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1453321	1.00[CHB][hapmap]
rs1470864	1.00[CHB][hapmap]
rs1597940	1.00[CHB][hapmap]
rs2167884	1.00[CHB][hapmap]
rs2305541	0.83[ASN][1000 genomes]
rs2602387	1.00[CHB][hapmap]
rs2602389	1.00[CHB][hapmap]
rs2603545	1.00[CHB][hapmap]
rs2603547	1.00[CHB][hapmap]
rs28444082	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28506837	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28588417	0.88[EUR][1000 genomes]
rs2924809	1.00[CHB][hapmap]
rs2971863	1.00[CHB][hapmap]
rs3762591	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59458664	0.85[ASN][1000 genomes]
rs6710645	1.00[CHB][hapmap]
rs6713866	0.90[EUR][1000 genomes]
rs6745134	1.00[CEU][hapmap]
rs6753062	1.00[CHB][hapmap]
rs6756068	1.00[CHB][hapmap]
rs73115402	0.82[AFR][1000 genomes]
rs73117507	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73117519	0.82[AFR][1000 genomes]
rs7422734	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7571288	1.00[CHB][hapmap]
rs7572257	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes]
rs7578898	1.00[CHB][hapmap]
rs838543	1.00[CHB][hapmap]
rs838544	1.00[CHB][hapmap]
rs838548	1.00[CHB][hapmap]
rs838549	1.00[CHB][hapmap]
rs838550	1.00[CHB][hapmap]
rs838551	1.00[CHB][hapmap]
rs838552	1.00[CHB][hapmap]
rs838555	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv584700	chr2:234199401-234364426	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234270000-234322400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:234272800-234313200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:234277600-234322200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:234294600-234318800	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr2:234295800-234318200	Weak transcription	K562	blood
6	chr2:234297200-234314600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr2:234297200-234316800	Weak transcription	Aorta	Aorta
8	chr2:234297200-234317000	Weak transcription	Placenta	Placenta
9	chr2:234297200-234317000	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr2:234297200-234317200	Weak transcription	Pancreas	Pancrea
11	chr2:234297200-234317400	Weak transcription	Brain Angular Gyrus	brain
12	chr2:234297200-234317400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr2:234297200-234318600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr2:234297200-234319000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr2:234297200-234319000	Weak transcription	Fetal Kidney	kidney
16	chr2:234297200-234319400	Weak transcription	Brain Hippocampus Middle	brain
17	chr2:234297200-234322000	Weak transcription	Hela-S3	cervix
18	chr2:234297200-234322200	Weak transcription	Brain Anterior Caudate	brain
19	chr2:234297400-234316200	Weak transcription	Fetal Lung	lung
20	chr2:234298000-234314600	Weak transcription	Stomach Smooth Muscle	stomach
21	chr2:234298000-234317200	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr2:234298600-234316200	Weak transcription	Colon Smooth Muscle	Colon
23	chr2:234299200-234316000	Weak transcription	Osteobl	bone
24	chr2:234299200-234319200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr2:234299200-234319200	Weak transcription	NHEK	skin
26	chr2:234300000-234318200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:234301200-234319800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr2:234301800-234315200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:234303000-234319000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:234305400-234313400	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr2:234305400-234317200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr2:234305400-234319000	Weak transcription	HSMMtube	muscle
33	chr2:234305400-234319200	Weak transcription	HSMM	muscle
34	chr2:234306400-234318000	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr2:234307200-234320200	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr2:234308200-234313400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr2:234308200-234318600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr2:234308200-234318800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr2:234308400-234316400	Weak transcription	Ovary	ovary
40	chr2:234308400-234317000	Weak transcription	Right Atrium	heart
41	chr2:234308400-234317200	Weak transcription	Left Ventricle	heart
42	chr2:234308400-234322200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr2:234308600-234317000	Weak transcription	Duodenum Smooth Muscle	Duodenum
44	chr2:234308800-234328400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr2:234309200-234316400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr2:234309200-234319000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr2:234309400-234313200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr2:234309400-234317000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr2:234309400-234317400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr2:234309400-234319200	Weak transcription	Brain Cingulate Gyrus	brain

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