Variant report

Variant	rs4310061
Chromosome Location	chr6:15259168-15259169
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:15256517..15259439-chr6:15263746..15265326,2	MCF-7	breast:
2	chr6:15256926..15259356-chr6:15400388..15402043,2	K562	blood:
3	chr6:15245709..15247287-chr6:15258599..15260921,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000008083	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1000399	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11962776	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11965232	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11966818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11968080	0.82[YRI][hapmap]
rs16876166	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16876169	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16876182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17712950	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57650809	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59272746	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60410720	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6941059	0.85[YRI][hapmap]
rs724971	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73359692	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73359693	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7769631	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830594	chr6:15171158-15261296	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv1027010	chr6:15201803-15425629	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription 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	27 gene(s)	inside rSNPs	diseases
3	nsv538140	chr6:15217899-15547127	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1030558	chr6:15234675-15449137	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv538141	chr6:15234675-15509163	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv538142	chr6:15243960-15404893	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15250000-15262000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
2	chr6:15250200-15259200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr6:15250400-15259200	Weak transcription	HMEC	breast
4	chr6:15251200-15279400	Weak transcription	A549	lung
5	chr6:15252400-15260000	Genic enhancers	Fetal Thymus	thymus
6	chr6:15253200-15262000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr6:15253200-15262200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr6:15253200-15269600	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr6:15253600-15261600	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr6:15253600-15262200	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr6:15253800-15261600	Enhancers	Brain Anterior Caudate	brain
12	chr6:15253800-15262000	Enhancers	Brain Cingulate Gyrus	brain
13	chr6:15254000-15261800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
14	chr6:15254000-15262000	Enhancers	Brain Hippocampus Middle	brain
15	chr6:15254200-15269600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr6:15254400-15259800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr6:15254600-15263200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr6:15254600-15264800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr6:15254800-15260200	Enhancers	H1 Cell Line	embryonic stem cell
20	chr6:15254800-15262800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr6:15254800-15264200	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr6:15254800-15269800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr6:15255000-15261200	Enhancers	Fetal Muscle Leg	muscle
24	chr6:15255200-15261600	Weak transcription	Placenta	Placenta
25	chr6:15255400-15259600	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr6:15255400-15261200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr6:15255800-15259800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr6:15256000-15259600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr6:15256000-15261600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr6:15256000-15261600	Enhancers	Brain Substantia Nigra	brain
31	chr6:15256000-15262000	Enhancers	HSMM	muscle
32	chr6:15256000-15264600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr6:15256200-15259200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr6:15256200-15259200	Weak transcription	Fetal Stomach	stomach
35	chr6:15256200-15262800	Weak transcription	Spleen	Spleen
36	chr6:15256200-15263800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr6:15256400-15259400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr6:15256400-15259400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr6:15256400-15261000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr6:15256400-15263200	Weak transcription	Esophagus	oesophagus
41	chr6:15256400-15263400	Weak transcription	Gastric	stomach
42	chr6:15256400-15264200	Weak transcription	HepG2	liver
43	chr6:15256400-15265400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr6:15256600-15262600	Genic enhancers	HUES48 Cell Line	embryonic stem cell
45	chr6:15256600-15263400	Enhancers	Muscle Satellite Cultured Cells	--
46	chr6:15256800-15259200	Weak transcription	Brain Germinal Matrix	brain
47	chr6:15256800-15259400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr6:15256800-15261400	Enhancers	Fetal Heart	heart
49	chr6:15256800-15261800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr6:15257000-15259200	Weak transcription	Thymus	Thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links