Variant report

Variant	rs4971029
Chromosome Location	chr1:151277259-151277260
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	1:151171193-151178589..1:151270864-151283078	K562	blood:
2	chr1:151276202..151278002-chr1:151279068..151281945,4	K562	blood:
3	chr1:151276165..151277813-chr1:151278370..151280878,2	MCF-7	breast:
4	chr1:151253847..151256191-chr1:151274577..151277583,3	K562	blood:
5	chr1:151273432..151279540-chr1:151311017..151317396,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143373	Chromatin interaction
ENSG00000232671	Chromatin interaction
ENSG00000143398	Chromatin interaction
ENSG00000143393	Chromatin interaction
ENSG00000224645	Chromatin interaction
ENSG00000143390	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1056847	0.90[JPT][hapmap]
rs10749660	0.85[JPT][hapmap]
rs10788801	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs10788803	0.91[JPT][hapmap]
rs10888408	0.91[JPT][hapmap]
rs10888409	0.91[JPT][hapmap]
rs10888410	0.91[JPT][hapmap]
rs11204785	0.85[JPT][hapmap]
rs11204791	0.91[JPT][hapmap]
rs11204798	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1536617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16827941	0.85[JPT][hapmap]
rs1752385	0.81[EUR][1000 genomes]
rs1752387	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1780582	0.85[EUR][1000 genomes]
rs1780587	0.84[EUR][1000 genomes]
rs2025900	0.80[CEU][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs2031797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2275900	0.91[JPT][hapmap]
rs2769266	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2769267	0.84[CEU][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes]
rs2769268	0.91[JPT][hapmap];0.81[EUR][1000 genomes]
rs2769269	0.81[EUR][1000 genomes]
rs2769273	0.84[CEU][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs2800946	0.89[CEU][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2800947	0.81[EUR][1000 genomes]
rs2800949	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2800950	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2800951	0.81[EUR][1000 genomes]
rs2800953	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs3811405	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs3811406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4246525	0.85[JPT][hapmap]
rs4520422	0.85[JPT][hapmap]
rs4636463	0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs4970944	0.85[JPT][hapmap]
rs4970948	0.91[JPT][hapmap]
rs4971013	0.85[JPT][hapmap]
rs4971018	0.85[JPT][hapmap]
rs4971023	0.86[JPT][hapmap]
rs4971027	0.91[JPT][hapmap]
rs4971028	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4971030	0.91[JPT][hapmap]
rs5022636	0.81[JPT][hapmap]
rs6587559	0.85[JPT][hapmap]
rs6587562	0.91[JPT][hapmap]
rs6678528	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs6686402	0.85[JPT][hapmap]
rs6695344	0.80[JPT][hapmap]
rs7527032	0.85[JPT][hapmap]
rs7532935	0.85[JPT][hapmap]
rs7539584	0.85[JPT][hapmap]
rs7544947	0.85[JPT][hapmap]
rs7545392	0.87[JPT][hapmap]
rs7552906	0.82[JPT][hapmap]
rs943637	0.90[JPT][hapmap]

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	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
2	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
3	nsv831570	chr1:151129020-151281778	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
4	esv2754960	chr1:151240542-151331304	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
5	esv34461	chr1:151240542-151411635	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
6	esv2753774	chr1:151240542-151411635	Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151256800-151281400	Strong transcription	Fetal Stomach	stomach
2	chr1:151257000-151281200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr1:151257000-151281800	Weak transcription	Right Atrium	heart
4	chr1:151257200-151283000	Strong transcription	Primary T helper cells fromperipheralblood	blood
5	chr1:151257200-151297600	Strong transcription	Dnd41	blood
6	chr1:151257400-151281200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:151257400-151281200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:151257400-151281800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:151257400-151282000	Strong transcription	Fetal Lung	lung
10	chr1:151257400-151282200	Strong transcription	Fetal Intestine Large	intestine
11	chr1:151257400-151282200	Strong transcription	Osteobl	bone
12	chr1:151257400-151283600	Strong transcription	Rectal Mucosa Donor 31	rectum
13	chr1:151257600-151281200	Strong transcription	Adipose Nuclei	Adipose
14	chr1:151257600-151281200	Strong transcription	Skeletal Muscle Male	skeletal muscle
15	chr1:151257600-151293600	Strong transcription	Brain Germinal Matrix	brain
16	chr1:151257800-151281600	Strong transcription	Skeletal Muscle Female	skeletal muscle
17	chr1:151257800-151282000	Strong transcription	Duodenum Mucosa	Duodenum
18	chr1:151258000-151283200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr1:151258000-151283600	Strong transcription	Lung	lung
20	chr1:151258200-151281400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr1:151258200-151281600	Strong transcription	Duodenum Smooth Muscle	Duodenum
22	chr1:151258200-151282000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:151258200-151297200	Strong transcription	Primary B cells from peripheral blood	blood
24	chr1:151258400-151281000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:151258400-151281800	Strong transcription	Rectal Smooth Muscle	rectum
26	chr1:151258400-151283000	Strong transcription	Colonic Mucosa	Colon
27	chr1:151258400-151293400	Strong transcription	Fetal Brain Female	brain
28	chr1:151258400-151297800	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr1:151258600-151282000	Strong transcription	Liver	Liver
30	chr1:151258600-151282000	Strong transcription	Left Ventricle	heart
31	chr1:151258800-151281400	Strong transcription	Placenta Amnion	Placenta Amnion
32	chr1:151258800-151281600	Strong transcription	NHLF	lung
33	chr1:151259600-151281800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr1:151260000-151298000	Strong transcription	Thymus	Thymus
35	chr1:151260400-151281200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr1:151261600-151283400	Strong transcription	Spleen	Spleen
37	chr1:151261600-151297800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr1:151262000-151298000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:151262400-151281800	Strong transcription	Fetal Intestine Small	intestine
40	chr1:151262400-151283400	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr1:151262400-151283600	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr1:151262400-151283800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr1:151262600-151281800	Strong transcription	Stomach Smooth Muscle	stomach
44	chr1:151262600-151284400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr1:151262600-151297600	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr1:151262800-151281000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr1:151262800-151282400	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr1:151262800-151282400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:151262800-151283400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:151262800-151283600	Strong transcription	Primary T cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links