Variant report

Variant	rs6493358
Chromosome Location	chr15:31241641-31241642
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:31234145..31235781-chr15:31240039..31242317,2	MCF-7	breast:

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10163148	0.83[CHB][hapmap]
rs10519726	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11070678	0.83[CHB][hapmap]
rs1133642	0.82[CHB][hapmap]
rs11852466	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11852722	0.90[YRI][hapmap]
rs12437677	0.91[ASN][1000 genomes]
rs12441456	0.89[ASN][1000 genomes]
rs12442021	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12442333	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12442823	0.91[ASN][1000 genomes]
rs1474381	0.83[CHB][hapmap]
rs1474382	0.83[CHB][hapmap]
rs16956341	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16956362	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16956366	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16956414	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs16956422	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs16956460	0.85[ASN][1000 genomes]
rs2113945	0.83[CHB][hapmap]
rs2272218	0.83[CHB][hapmap]
rs2272219	0.83[CHB][hapmap]
rs2293319	0.83[CHB][hapmap]
rs2293320	0.83[CHB][hapmap]
rs28487996	0.87[ASN][1000 genomes]
rs28693590	0.83[CHB][hapmap]
rs2949575	0.83[CHB][hapmap]
rs2949576	0.83[CHB][hapmap]
rs2949578	0.83[CHB][hapmap]
rs2955787	0.83[CHB][hapmap]
rs2955791	0.83[CHB][hapmap]
rs2959049	0.83[CHB][hapmap]
rs36042462	0.89[ASN][1000 genomes]
rs3743231	0.83[CHB][hapmap]
rs3743232	0.91[ASN][1000 genomes]
rs3784588	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4779796	0.83[CHB][hapmap]
rs4779797	0.83[CHB][hapmap]
rs7161812	0.82[CHB][hapmap]
rs7164939	1.00[CHB][hapmap]
rs7169064	0.83[CHB][hapmap]
rs7175354	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs7175951	0.83[CHB][hapmap]
rs7176351	0.83[CHB][hapmap]
rs7178375	0.83[CHB][hapmap]
rs7178533	0.83[CHB][hapmap]
rs73368444	0.89[ASN][1000 genomes]
rs8041717	0.83[CHB][hapmap]
rs871312	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs872843	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs964925	0.91[CHB][hapmap]
rs9806159	0.83[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427955	chr15:30467980-31273174	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv531138	chr15:30653877-31609679	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv916936	chr15:30921917-31337510	Active TSS Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv525795	chr15:30936285-31324531	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS 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 target site	35 gene(s)	inside rSNPs	diseases
5	nsv533434	chr15:30938215-31244225	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv903831	chr15:30986051-31723279	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
7	nsv1046874	chr15:31008133-31294654	Enhancers Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv1054147	chr15:31014507-31972706	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
9	nsv542306	chr15:31014507-31972706	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
10	nsv832951	chr15:31131239-31304469	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
11	nsv1039037	chr15:31140415-31277268	Strong transcription ZNF genes & repeats Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
12	nsv542309	chr15:31140415-31277268	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
13	nsv1036018	chr15:31140415-31544888	Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
14	nsv521842	chr15:31140700-31272670	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
15	nsv903834	chr15:31179534-31293774	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
16	esv33507	chr15:31183324-31471023	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
17	nsv832952	chr15:31204426-31333998	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:31200400-31242200	Strong transcription	Primary T cells from cord blood	blood
2	chr15:31200600-31254800	Strong transcription	Primary T helper cells fromperipheralblood	blood
3	chr15:31216600-31245800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr15:31221000-31246800	Strong transcription	Cortex derived primary cultured neurospheres	brain
5	chr15:31225400-31246200	Strong transcription	Stomach Smooth Muscle	stomach
6	chr15:31225400-31255800	Strong transcription	Fetal Intestine Large	intestine
7	chr15:31225600-31246000	Strong transcription	Placenta	Placenta
8	chr15:31225600-31246200	Strong transcription	Adipose Nuclei	Adipose
9	chr15:31225600-31253800	Strong transcription	Dnd41	blood
10	chr15:31225800-31245400	Strong transcription	Skeletal Muscle Female	skeletal muscle
11	chr15:31225800-31246200	Strong transcription	GM12878-XiMat	blood
12	chr15:31225800-31256000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr15:31226000-31245400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr15:31226000-31246000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr15:31226000-31255800	Strong transcription	Fetal Stomach	stomach
16	chr15:31226000-31258800	Strong transcription	Duodenum Mucosa	Duodenum
17	chr15:31226200-31246400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr15:31226200-31246800	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr15:31226200-31269200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr15:31226400-31260800	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr15:31226600-31245400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr15:31226600-31246000	Strong transcription	Ovary	ovary
23	chr15:31226600-31254400	Strong transcription	Fetal Thymus	thymus
24	chr15:31226600-31255200	Strong transcription	Duodenum Smooth Muscle	Duodenum
25	chr15:31226800-31244200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr15:31226800-31245600	Strong transcription	Muscle Satellite Cultured Cells	--
27	chr15:31227000-31269600	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr15:31227200-31255800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr15:31227200-31258800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr15:31227400-31241800	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr15:31228000-31246000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr15:31228200-31246000	Strong transcription	Fetal Muscle Trunk	muscle
33	chr15:31228400-31245800	Strong transcription	Osteobl	bone
34	chr15:31228400-31246000	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr15:31228400-31253600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr15:31228400-31254400	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr15:31228400-31254600	Strong transcription	Thymus	Thymus
38	chr15:31228600-31241800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr15:31228600-31253200	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr15:31228600-31258800	Strong transcription	Rectal Mucosa Donor 29	rectum
41	chr15:31228800-31245400	Strong transcription	Skeletal Muscle Male	skeletal muscle
42	chr15:31228800-31246000	Strong transcription	HSMM	muscle
43	chr15:31229000-31245400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr15:31229000-31254800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr15:31229200-31246400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr15:31229200-31261000	Strong transcription	Primary B cells from peripheral blood	blood
47	chr15:31229400-31245000	Strong transcription	HSMMtube	muscle
48	chr15:31230400-31258800	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr15:31230600-31242000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr15:31230600-31245200	Strong transcription	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links