Variant report

Variant	rs2465405
Chromosome Location	chr15:56532690-56532691
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	EP300	chr15:56532668-56532963	GM12878	blood:	n/a	n/a
2	BATF	chr15:56532684-56532911	GM12878	blood:	n/a	n/a
3	MXI1	chr15:56532128-56532985	GM12878	blood:	n/a	n/a
4	CUX1	chr15:56532673-56532873	GM12878	blood:	n/a	n/a
5	CHD1	chr15:56532644-56532958	GM12878	blood:	n/a	n/a
6	BHLHE40	chr15:56532584-56533011	GM12878	blood:	n/a	n/a
7	POLR2A	chr15:56532640-56533026	MCF10A-Er-Src	breast:	n/a	n/a
8	NFIC	chr15:56532432-56533076	GM12878	blood:	n/a	n/a
9	MEF2A	chr15:56532598-56532909	GM12878	blood:	n/a	chr15:56532889-56532904 chr15:56532891-56532906
10	E2F4	chr15:56532638-56533256	MCF10A-Er-Src	breast:	n/a	chr15:56532915-56532926
11	RUNX3	chr15:56532590-56533033	GM12878	blood:	n/a	n/a
12	FOS	chr15:56532640-56532857	MCF10A-Er-Src	breast:	n/a	chr15:56532819-56532831
13	EP300	chr15:56532610-56532931	GM12878	blood:	n/a	n/a
14	MEF2A	chr15:56532558-56532971	GM12878	blood:	n/a	chr15:56532575-56532591 chr15:56532889-56532904 chr15:56532891-56532906 chr15:56532576-56532591 chr15:56532577-56532592
15	FOS	chr15:56532384-56532862	MCF10A-Er-Src	breast:	n/a	chr15:56532819-56532831

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:56529793..56531409-chr15:56531688..56534062,2	MCF-7	breast:

Variant related genes	Relation type
TEX9	TF binding region

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

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

rs_ID	r²[population]
rs10152826	0.84[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap];0.89[EUR][1000 genomes]
rs10162834	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10163161	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10438327	0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.83[LWK][hapmap]
rs1072358	0.80[EUR][1000 genomes]
rs11632218	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs11853962	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap]
rs11855937	0.88[CEU][hapmap];0.81[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap]
rs11856691	0.80[AMR][1000 genomes]
rs11858173	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11858245	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12324006	0.80[EUR][1000 genomes]
rs12898789	0.80[EUR][1000 genomes]
rs12899534	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12901182	0.88[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap]
rs12907445	0.80[EUR][1000 genomes]
rs12908839	0.88[CEU][hapmap];0.86[JPT][hapmap]
rs13379820	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1426070	0.90[MEX][hapmap];0.89[TSI][hapmap]
rs1520532	0.80[EUR][1000 genomes]
rs17238601	0.82[ASW][hapmap];0.96[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.82[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes]
rs17238691	0.88[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap]
rs17819384	0.96[LWK][hapmap];1.00[YRI][hapmap]
rs1829543	0.96[CEU][hapmap];0.95[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2247838	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2460649	0.92[CEU][hapmap];0.85[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2465969	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2554287	0.88[CEU][hapmap]
rs2584689	0.96[CEU][hapmap];0.89[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2682030	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2682031	0.95[CEU][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2682032	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2682048	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2682050	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.84[ASN][1000 genomes]
rs2682055	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2713922	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2713934	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2713937	0.96[CEU][hapmap];0.83[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2713939	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2718921	0.88[CEU][hapmap]
rs2718924	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2718934	0.83[CHB][hapmap]
rs2718947	0.86[EUR][1000 genomes]
rs2725856	0.88[CEU][hapmap]
rs2725871	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.84[ASN][1000 genomes]
rs28621861	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2947023	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34684027	0.80[EUR][1000 genomes]
rs35131119	0.80[EUR][1000 genomes]
rs35187662	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35840822	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs35968448	0.80[EUR][1000 genomes]
rs4774238	0.80[EUR][1000 genomes]
rs4774854	0.88[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap]
rs56274791	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62044114	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6493844	0.89[EUR][1000 genomes]
rs7163807	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs748344	0.80[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.82[MEX][hapmap];0.89[MKK][hapmap];0.84[TSI][hapmap];0.86[ASN][1000 genomes]
rs767142	0.80[EUR][1000 genomes]
rs8032826	0.89[EUR][1000 genomes]
rs8041422	0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.92[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs894415	0.96[CEU][hapmap];0.92[GIH][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]

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	nsv833019	chr15:56486029-56649933	Transcr. at gene 5' and 3' Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv569547	chr15:56504598-56572176	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56508000-56534400	Weak transcription	Fetal Heart	heart
2	chr15:56509000-56533600	Weak transcription	Osteobl	bone
3	chr15:56514000-56535000	Weak transcription	Pancreas	Pancrea
4	chr15:56514800-56534800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr15:56522800-56533600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr15:56524600-56533800	Weak transcription	Aorta	Aorta
7	chr15:56524600-56534800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr15:56524800-56533600	Weak transcription	Brain Hippocampus Middle	brain
9	chr15:56524800-56533600	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr15:56524800-56533800	Weak transcription	Ovary	ovary
11	chr15:56524800-56534800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:56524800-56534800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr15:56524800-56534800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr15:56524800-56534800	Weak transcription	Small Intestine	intestine
15	chr15:56524800-56535000	Weak transcription	Esophagus	oesophagus
16	chr15:56525000-56533400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr15:56525000-56533600	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr15:56525400-56533600	Weak transcription	Brain Substantia Nigra	brain
19	chr15:56525400-56534800	Weak transcription	Placenta	Placenta
20	chr15:56525400-56535000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr15:56525600-56533600	Weak transcription	Fetal Stomach	stomach
22	chr15:56525600-56535000	Weak transcription	Lung	lung
23	chr15:56525800-56533200	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr15:56525800-56533400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr15:56525800-56533800	Weak transcription	Fetal Muscle Leg	muscle
26	chr15:56526000-56533400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr15:56526000-56533400	Weak transcription	Fetal Intestine Small	intestine
28	chr15:56526000-56533400	Weak transcription	Thymus	Thymus
29	chr15:56526000-56533600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr15:56526000-56533600	Weak transcription	Brain Angular Gyrus	brain
31	chr15:56526000-56533600	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr15:56526200-56533200	Weak transcription	Hela-S3	cervix
33	chr15:56526200-56534200	Weak transcription	Fetal Intestine Large	intestine
34	chr15:56526400-56533600	Weak transcription	HepG2	liver
35	chr15:56526600-56533200	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr15:56526600-56533400	Weak transcription	Liver	Liver
37	chr15:56526600-56533600	Weak transcription	Fetal Kidney	kidney
38	chr15:56526800-56532800	Weak transcription	HUVEC	blood vessel
39	chr15:56526800-56533200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr15:56526800-56533400	Weak transcription	Primary B cells from peripheral blood	blood
41	chr15:56526800-56533600	Weak transcription	Fetal Thymus	thymus
42	chr15:56526800-56533800	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr15:56527000-56533200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr15:56527000-56533400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr15:56527800-56533400	Weak transcription	Primary B cells from cord blood	blood
46	chr15:56527800-56533800	Weak transcription	Psoas Muscle	Psoas
47	chr15:56528000-56533400	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr15:56528000-56533400	Weak transcription	Duodenum Mucosa	Duodenum
49	chr15:56528200-56533200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr15:56528200-56533400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links