Variant report

Variant	rs16902835
Chromosome Location	chr5:36225246-36225247
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:36223256..36225953-chr5:36698495..36700466,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10454863	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10512639	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10512640	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs10941277	0.84[ASN][1000 genomes]
rs10941278	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10941279	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10941281	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10941285	0.88[CEU][hapmap]
rs11737918	0.88[ASN][1000 genomes]
rs11738615	0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs11739323	0.87[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11744207	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11745827	0.88[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11747546	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11952882	0.82[EUR][1000 genomes]
rs12186384	0.86[EUR][1000 genomes]
rs12189205	0.85[EUR][1000 genomes]
rs12522905	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13154462	0.87[EUR][1000 genomes]
rs13162876	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs13163528	0.87[EUR][1000 genomes]
rs13174907	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs13178531	0.82[EUR][1000 genomes]
rs13179201	0.86[EUR][1000 genomes]
rs13185969	0.87[EUR][1000 genomes]
rs1363840	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2362977	0.87[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2362979	0.87[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2432204	0.86[ASN][1000 genomes]
rs249272	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28610396	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3088073	0.92[CEU][hapmap]
rs35161198	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35647151	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3761973	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3789758	0.87[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3933496	0.88[ASN][1000 genomes]
rs4869475	0.92[CEU][hapmap]
rs62356073	0.82[EUR][1000 genomes]
rs6451261	0.83[EUR][1000 genomes]
rs67061065	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67399512	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6879127	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6881318	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6884331	0.88[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6890702	0.88[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs72744549	0.92[ASN][1000 genomes]
rs72744564	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72744565	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72744587	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7703895	0.92[CEU][hapmap]
rs7710062	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7716788	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7719357	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs7719686	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs7723157	1.00[CEU][hapmap];0.83[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	nsv830262	chr5:36074311-36293872	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	63 gene(s)	inside rSNPs	diseases
2	nsv1015638	chr5:36203646-36312576	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:36172000-36229200	Weak transcription	Colonic Mucosa	Colon
2	chr5:36179000-36230000	Weak transcription	Psoas Muscle	Psoas
3	chr5:36190600-36227400	Weak transcription	Thymus	Thymus
4	chr5:36191800-36230000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:36192600-36227800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr5:36196600-36236600	Weak transcription	GM12878-XiMat	blood
7	chr5:36198000-36238400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr5:36200000-36229600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr5:36200200-36239400	Weak transcription	Fetal Brain Male	brain
10	chr5:36201200-36230200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr5:36201400-36240000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr5:36203800-36227000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:36204000-36227000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr5:36205200-36226800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr5:36212400-36226800	Strong transcription	Rectal Mucosa Donor 29	rectum
16	chr5:36213200-36230200	Weak transcription	Brain Germinal Matrix	brain
17	chr5:36213200-36237000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr5:36213400-36227600	Weak transcription	NH-A	brain
19	chr5:36214800-36226200	Strong transcription	Primary T cells fromperipheralblood	blood
20	chr5:36215200-36236600	Weak transcription	Small Intestine	intestine
21	chr5:36215800-36237800	Weak transcription	HMEC	breast
22	chr5:36216400-36225800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr5:36216800-36228400	Weak transcription	HUVEC	blood vessel
24	chr5:36219000-36226600	Strong transcription	Skeletal Muscle Female	skeletal muscle
25	chr5:36219000-36227000	Strong transcription	HepG2	liver
26	chr5:36219200-36226600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr5:36219200-36226800	Strong transcription	Adipose Nuclei	Adipose
28	chr5:36219400-36226000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr5:36219400-36226600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr5:36219600-36230000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr5:36219800-36227000	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr5:36220200-36226600	Strong transcription	Brain Anterior Caudate	brain
33	chr5:36220400-36226000	Strong transcription	Brain Cingulate Gyrus	brain
34	chr5:36220400-36226200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr5:36220600-36226600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr5:36220800-36226200	Strong transcription	Primary T cells from cord blood	blood
37	chr5:36221000-36226600	Strong transcription	Liver	Liver
38	chr5:36221000-36230200	Weak transcription	K562	blood
39	chr5:36221200-36230000	Weak transcription	HSMMtube	muscle
40	chr5:36221200-36230400	Weak transcription	Lung	lung
41	chr5:36221200-36238800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr5:36221400-36226000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr5:36221400-36226800	Weak transcription	Right Ventricle	heart
44	chr5:36221400-36229600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr5:36221600-36225400	Weak transcription	Primary B cells from peripheral blood	blood
46	chr5:36221600-36226800	Weak transcription	Esophagus	oesophagus
47	chr5:36221600-36230000	Weak transcription	Pancreas	Pancrea
48	chr5:36221600-36230200	Weak transcription	Gastric	stomach
49	chr5:36221600-36232600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr5:36221600-36235600	Weak transcription	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links