Variant report

Variant	rs496499
Chromosome Location	chr15:41398316-41398317
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	FOS	chr15:41398299-41398499	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr15:41398273-41398425	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr15:41398199-41398525	HepG2	liver:	n/a	n/a
4	FOS	chr15:41398314-41398377	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:41397401..41399850-chr15:41405689..41409184,4	MCF-7	breast:
2	chr15:41396623..41400831-chr15:41405034..41410190,10	K562	blood:
3	chr15:41395985..41399241-chr15:41408048..41410714,4	K562	blood:
4	chr15:41396638..41398634-chr15:41406036..41407580,2	K562	blood:

Variant related genes	Relation type
CYCSP2	TF binding region
ENSG00000128908	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10152296	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11070319	1.00[ASW][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes]
rs11070320	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11630905	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs16971263	0.88[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes]
rs16971264	1.00[MEX][hapmap]
rs16971413	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs16971463	1.00[ASW][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16971507	1.00[MEX][hapmap]
rs2007255	1.00[MEX][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes]
rs2412573	0.86[YRI][hapmap]
rs2412599	0.82[LWK][hapmap];1.00[TSI][hapmap]
rs2412600	0.84[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap]
rs28455970	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28528813	0.89[AMR][1000 genomes]
rs2899010	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2925344	1.00[MEX][hapmap]
rs2925348	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs2925349	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2927067	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2928147	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2928149	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2928150	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2928154	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2947492	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs2947495	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2947496	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs2955812	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3101435	0.96[YRI][hapmap];0.83[AMR][1000 genomes]
rs3101438	1.00[ASW][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs3101440	1.00[MEX][hapmap]
rs3101441	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs4468583	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs474351	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs480549	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs487779	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4923894	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4923895	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs4924533	1.00[ASW][hapmap];0.98[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs4924534	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs513680	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs518137	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs525551	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs538903	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs56955512	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57008457	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs57385441	1.00[AMR][1000 genomes]
rs58142514	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs59405359	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs690773	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs691069	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs691445	1.00[EUR][1000 genomes]
rs691722	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs692703	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs7162003	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs7165020	1.00[GIH][hapmap]
rs7167166	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7169092	1.00[MEX][hapmap]
rs7172555	1.00[ASW][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7173146	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7174513	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs7178308	1.00[GIH][hapmap]
rs7183191	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes]
rs73399092	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8030958	1.00[MEX][hapmap]
rs8032956	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8034461	0.94[AMR][1000 genomes]
rs8035532	1.00[AMR][1000 genomes]
rs8043232	0.88[ASW][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes]
rs9806344	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569229	chr15:41361138-41483682	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	nsv904107	chr15:41361138-41493013	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv569230	chr15:41384649-41483682	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
4	nsv904108	chr15:41384649-41486990	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41361200-41407200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr15:41383200-41406800	Weak transcription	A549	lung
3	chr15:41383800-41407400	Weak transcription	Esophagus	oesophagus
4	chr15:41384000-41407400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:41384400-41407400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr15:41385200-41406000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr15:41386200-41398400	Weak transcription	Gastric	stomach
8	chr15:41386200-41407400	Weak transcription	Aorta	Aorta
9	chr15:41386600-41407400	Weak transcription	Colonic Mucosa	Colon
10	chr15:41386800-41398400	Weak transcription	Brain Angular Gyrus	brain
11	chr15:41386800-41405400	Weak transcription	Spleen	Spleen
12	chr15:41386800-41406800	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr15:41386800-41406800	Weak transcription	Right Ventricle	heart
14	chr15:41386800-41407000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr15:41386800-41407200	Weak transcription	HSMMtube	muscle
16	chr15:41386800-41407400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr15:41387000-41400400	Weak transcription	Brain Germinal Matrix	brain
18	chr15:41387200-41399200	Weak transcription	GM12878-XiMat	blood
19	chr15:41387200-41406000	Weak transcription	Brain Hippocampus Middle	brain
20	chr15:41387200-41406600	Weak transcription	Pancreas	Pancrea
21	chr15:41387400-41407200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr15:41388000-41398400	Weak transcription	Primary hematopoietic stem cells	blood
23	chr15:41388000-41406600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr15:41388200-41406600	Weak transcription	Adipose Nuclei	Adipose
25	chr15:41388400-41406400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
26	chr15:41388600-41398400	Weak transcription	Left Ventricle	heart
27	chr15:41388600-41400200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr15:41388600-41400800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr15:41388600-41402200	Weak transcription	Fetal Muscle Trunk	muscle
30	chr15:41388600-41404200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr15:41388600-41405600	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr15:41388600-41405800	Weak transcription	Colon Smooth Muscle	Colon
33	chr15:41388600-41406600	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr15:41388600-41406600	Weak transcription	Ovary	ovary
35	chr15:41388600-41406600	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr15:41388600-41406800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr15:41388600-41406800	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr15:41388600-41406800	Weak transcription	Fetal Brain Female	brain
39	chr15:41388600-41406800	Weak transcription	Fetal Lung	lung
40	chr15:41388600-41407000	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr15:41388600-41407000	Weak transcription	Fetal Kidney	kidney
42	chr15:41388600-41407200	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr15:41388600-41407200	Weak transcription	Brain Anterior Caudate	brain
44	chr15:41388600-41407400	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr15:41388800-41398400	Weak transcription	Thymus	Thymus
46	chr15:41388800-41400400	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr15:41388800-41400800	Weak transcription	Primary T cells from cord blood	blood
48	chr15:41388800-41401000	Weak transcription	Fetal Muscle Leg	muscle
49	chr15:41388800-41401400	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr15:41388800-41402600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links